Chapter Nine: Patterns of Inheritance

Questions:

1. What are most human genetic disorders caused by?
2. What are some dominant disorders?
3. What is the chromosome theory of inheritance?

Answers:

1. Most human genetic disorders are recessive.  They range in severity from relatively mild, such as albinism (lack of pigmentation), to life-threatening, such as cystic fibrosis.  Most people who have recessive disorders are born to normal parents who are both heterozygotes.  That is, they are carriers of the recessive allele for the disorder but are phenotypically normal. 
2. One serious dominant disorder is achondroplasia, a form of dwarfism.  In people with this disorder, the head and torso of the body develop normally, but the arms and legs are short.  Another is Huntington's Disease, a degenerative disorder of the nervous system that usually does not appear until 35 to 45 years of age.
3. The chromosome theory of inheritance states that genes occupy specific loci on chromosomes and it is the chromosomes that undergo segregation and independent assortment during meiosis.  Thus, it is the behavior of chromosomes during meiosis and fertilization that accounts for inheritance patterns.

Important Facts:

1. The rule of addition is the probability that an event can occur in two or more alternative ways is the sum of the separate probabilities of the different ways. 
2. An organism's appearance does not always reveal its genetic composition.  An organism's physical traits are called its physical traits.  It's genetic makeup is its genotype.
3. The law of independent assortment states that each pair of alleles segregates independently of other pairs of alleles during gamete formation.
4. Pleiotropy is the property that most genes influence multiple characters.
5. Polygenic inheritance are the additive effects of two or more genes on a single phenotypic character.

Key Terms:
Hybrids- the offspring of two different varieties.
P Generation- the true-breeding parental plants.
F1 Generation- P generation's hybrid offspring.
F2 Generation- offspring when F1 plants self-fertilize or fertilize each other.
Alleles- the alternative versions of a gene.
Homozygous- when an organism has two identical alleles for a gene, it is homozygous for that gene.
Heterozygous- when an organism has two different alleles for a gene, it is heterozygous for that gene.
Dominant allele- allele that determines the organism's appearance.
Recessive allele- allele that has no noticeable affect on the organism's appearance.
Law of Segregation-  A sperm or egg carries only one allele for each inherited character because allele pairs separate from each other during the production of gametes.

Diagram: This diagram is used to predict an outcome of a particular cross or breeding experiment. It is named after Reginald C. Punnett, who devised the approach, and is used by biologists to determine the probability of an offspring having a particular genotype. The Punnett square is a summary of every possible combination of one maternal allele with one paternal allele for each gene being studied in the cross.

Relevant Video:
http://www.youtube.com/watch?v=oVl8OH_7QSc&feature=related

Summary: This chapter focuses first on Mendelian genetics and crosses.  It then discusses more human genetics before moving on to genes and chromosomes.  It talks about the chromosomal basis of inheritance.  The chapter then details sex chromosomes and sex-linked genes.

Chapter Eight: The Cellular Basis of Reproduction and Inheritance

Questions:

1. What are the various steps of mitosis and meiosis?
2. What are the two methods of reproduction?
3. What is the difference between cytokinesis in plant and animal cells?

Answers:

1. The steps of mitosis are interphase, prophase, prometaphase, metaphase, anaphase, telophase, and cytokinesis.  Meiosis first begins with meiosis I.  During meiosis I, prophase I, metaphase I, anaphase I, and telophase I all occur.  Meiosis II follows meiosis I without chromosome duplication.
2. The two methods of reproduction are asexual reproduction and sexual reproduction.  In asexual reproduction, offspring are identical to the original cell or organism.  The offspring also inherits all  its genes from one parent.  In sexual reproduction, offspring are similar to parents, but show variations in their traits and involve the inheritance of unique sets of genes from two different parents.
3. A ring of microfilaments pinches an animal cell in two, a process called cleavage.  In a plant cell, membranous vesicles form a disk called the cell plate at the midline of the parent cell, cell plate membranes fuse with the plasma membrane, and a cell wall grows in the space.  

Important Facts:

• Somatic cells have pairs of homologous chromosomes, receiving one member of each pair from each parent.  Homologous chromosomes are matched in length, centromere position and gene locations.  
• Cancer cells escape control on the cell cycle.  They divide rapidly, often in the absence of growth factors.  They spread to other tissues through the circulatory system.  The growth is not inhibited by other cells and tumors form.
• The factors that control cell division include: presence of essential nutrients, growth factors, proteins that simulate division, presence of other cells causes density-dependent inhibition, and contact with a solid surface, as most cells show anchorage dependence.
• Separation of homologous chromosomes during meiosis can lead to genetic differences between gametes.  Homologous chromosomes may have different versions of a gene at the same locus.  One version was inherited from the maternal parent, and the other came from the paternal parent.  Since homologues move to opposite poles during anaphase I, gametes receive either the paternal or maternal version of the gene.
• An imbalance in chromosome number results in Down Syndrome, which is characterized by characteristic facial features, susceptibility to disease, shortened life span, mental retardation, and variation in characteristics.

Key Terms:
Fertilization- the union of sperm and egg
Chromatin- DNA and proteins.
Cell Cycle- an ordered sequence of events for cell division.  Consists or interphase and Mitotic phase.
Interphase- duplication of cell contents.
Mitotic phase- division of cell.  Includes mitosis (division of the nucleus) and cytokinesis (division of cytoplasm)
Centrosomes- Structures in the cytoplasm that produce a mitotic spindle required to divide the chromosomes.  They organize micro-tubule arrangement and contain a pair of centrioles in animal cells.
Cell Cycle Control System- A set of molecules, including growth factors, that triggers and coordinates events of the cell cycle.
Diploid Cells- have two homologous sets of chromosomes.
Haploid Cells- have one set of chromosomes.
Nondisjunction- the failure of chromosomes or chromatids to separate during meiosis.


Relevant Diagram:  This diagram shows the whole process of meiosis.  Meiosis is the process of cell division in germ line cells to form gametes. This process furthers sexual reproduction because each gamete has half the number of chromosomes of normal cells, so that when two gametes (one from each parent) combine, the correct number of chromosomes is preserved in the resulting zygote organism. This process is unlike mitosis, where the cells are simply replicated, preserving the number chromosomes.

Relevant Video:
http://www.youtube.com/watch?v=BFWelOJ7fW0

Summary:
This chapter mainly discusses cell division/reproduction.  The chapter begins with mitosis, detailing first the role of chromosomes and then moving on to the different phases of mitosis.  It talks about cell cycle control and then moves on to meiosis and homologous chromosomes.  The many phases of meiosis are discussed in great detail.  The chapter then finishes with genetic variation and chromosome number which directly affects mutation.

Chapter Seven: Photosynthesis: Using Light to Make Food

Questions:

1. What are the similarities and differences between the two photo systems in photosynthesis?
2. Why does a poison that inhibits an enzyme of the Calvin cycle also inhibit the light reactions?
3. How might phytochemicals benefit a cell?

Answers:

1. Both photosystems have primary accepters and both accept light power from electrons.  They both  take place in the thylakoid membrane.  They both use ATP.  Photosystem 2 takes place before Photosystem 1.  They also use different wavelengths.  Photosystem 2 takes in water and releases oxygen and hydrogen.  Photosystem 1 does not do this.    
2. The light reactions require ADP and NADP+, which are not recycled from ATP and NADPH when the Calvin cycle stops.  
3. Phytochemicals can act as antioxidants that protect from reactive forms of oxidative molecules.

Important Facts:

1. Photosynthesis occurs in two metabolic stages.  One stage involves the light reactions.  H+ ions reduce NADP+ to NADPH, which is an electron carrier similar to NADH.  The Calvin cycle is the second stage that occurs in the stroma.  It is a cyclic series of reactions that builds sugar molecules from CO2......NADPH produced by the light reactions provides the electrons for reducing carbon in the Calvin cycle.  ATP from the light reactions provides chemical energy for the Calvin cycle, which is often known as a dark reaction.
2. In photosynthesis, electrons gain energy by being boosted up an energy hill.  Light energy captured by chlorophyll molecules provides the boost for the electrons.  As a result, light energy is converted to chemical energy, which is stored in the chemical bonds of sugar molecules.
3. Cellular respiration uses redox reactions to harvest the chemical energy stored in a glucose molecule.  This is accomplished by oxidizing the sugar and reducing O2 to H2O.  The electrons lose potential as they travel down an energy hill, the electron transport system.  In contrast, the food producing redox reactions of photosynthesis reverse the flow and involve an uphill climb.
4. Chemiosmosis is the mechanism that not only is involved in oxidative phosphorylation in mitochondria but also generates ATP in chloroplasts.  ATP is generated because  the electron transport chain produces a concentration gradient of hydrogen ions across a membrane.  ATP synthase couples the flow of H+ to the phosphorylation of ADP.  The chemiosmotic production of ATP in photosynthesis is called phosphorylation.
5. The energy released by electrons is conserved as it is passed from one molecule to another.  All of the components to accomplish this are organized in thylakoid membranes in clusters called photosystems.  Photosystems are light-harvesting complexes surrounding a reaction center complex.  Energy is passed from molecule to molecule within the photosystem.  The energy finally reaches the reaction center where a primary electron acceptor accepts these electrons and consequently becomes reduced.  This solar- powered transfer of an electron from the reaction center pigment to the primary electron acceptor is the first step of the light reactions.
   

Key Terms: 
Photosynthesis- Process that converts solar energy to chemical energy.  Plants use water and atmospheric carbon dioxide to produce a simple sugar and liberate oxygen.  This sugar is food for humans for and animals.
Autotroph- an organism that makes its own food, thereby sustaining itself without eating other organsims or their molecules.
Cloroplasts- organelles consisting of photosynthetic pigments, enzyme, and other molecules grouped together.
Chlorophyll- a green pigment located within the chloroplasts of plants, algae, and certain prokaryotes.
Electromagnetic Spectrum- the entire spectrum of radiation.
Mesophyll- the middle layer of tissue inside a leaf.
Photoautograph- an organism that obtains energy from sunlight and carbon from CO2 by photosynthesis.
Thylakoid- one of the number of disk-shaped membranous sacs inside a chloroplast.
Stomata- tiny pores in the leaf that allow carbon dioxide to enter and oxygen to exit.
Stroma- the dense fluid within the chloroplast that is contained in two membranes.

Diagram: The light-dependent reactions are the first stage of photosynthesis, the process by which plants capture and store energy from sunlight. In this proces, light energy is converted into chemical energy, in the form of the energy-carrying molecules ATP and NADPH.

Relevant Video: http://www.youtube.com/watch?v=GR2GA7chA_c

Summary: This chapter begins by detailing the stages of photosynthesis.  It then continues to discuss the light reactions and the converting of solar energy to chemical energy.  It mentions photosystems and photophosphorylation.  The chapter then discusses the Calvin cycle and the converting of CO2 to sugars.  It details C3, C4, and CAM plants before discussing solar radiation and the Earth's atmosphere.

Chapter Six: How Cells Harvest Chemical Energy

Questions:

1. What are the three different catagories of cellular poisons that affect cellular respiration?
2. What are the two common types of fermentation? Why are they important?
3. What are obligate anaerobes?

Answers:

1. The first category blocks the electron transport chain.  Examples of these are rotenone, cyanide and carbon monoxide.  The second inhibits ATP synthase (oligomycin).  The third makes the membrane leaky to hydrogen ions (dinitrophenal).
2. The two common types of fermentation are alcohol fermentation and lactic acid fermentation.  Fermentation is important because it allows a cell to continue to produce ATP without the use of oxygen, that is, under anaerobic conditions.
3. Obligate Anaerobes are prokaryotes that live in stagnant ponds or deep in the soil because they require anaerobic conditions and are poisoned by oxygen.

Important Facts:

1. Cellular respiration equation shows the changes in hydrogen atom distribution.  Glucose loses its hydrogen atoms and is converted to CO2.  As this happens, O2 gains two hydrogen atoms, while losing an oxygen atom.  This means that this reaction is a redox reaction.
2. Glycolysis begins respiration by breaking glucose, a six carbon molecule, into two molecules of a three-carbon compound called pyruvate.  This stage occurs in the cytoplasm.  The second stage is the Citric Acid cycle or Krebs cycle.  It breaks down pyruvate into carbon dioxide and supplies the next stage with electrons.  This stage occurs in the mitochondria.  During Oxidative phosphorylation, electrons are shuttled through the electron transport chain.  It also produces ATP with chemiosmosis.  This stage occurs in the membrane of the mitochondria.
3. Catabolic pathways occur when molecules are broken down and their energy is released.  Two types of catabolism are fermentation (the partial degradation of sugars that occurs without the use of oxygen) and cellular respiration.
4. Hydrogen ions flow back down their gradient through a channel in the transmembrane protein known as ATP synthase.  ATP synthase harnesses the proton motive force (the gradient of hydrogen ions) to phosphorylate ADP, forming ATP.  The proton motive force is in place because the inner membrane of the mitochondria is impermeable to hydrogen ions.  Electrons are held behind the inner membrane with their only exit the ATP synthase.
5. In alcohol fermentation, pyruvate is converted to ethanol, releasing CO2 and oxidizing NADH in the process to create more NAD+.

Key Terms:

Cellular Respiration- the aerobic harvesting of energy from sugar molecules by cells.

Oxidative Phosphorylation- Step 3 of cellular respiration.  Involves the electron transport chain and chemiosmosis.  NADH and FADH2 shuttle electrons to the electron transport chain imbedded in the inner mitochondrion membrane.  This is where most of the ATP for a cell is produced.  The energy released by the downhill fall of electrons from NADH and FADH2 to O2 is used to phosphorylate ADP.

ATP Synthases- protein complexes built into the inner membrane that synthesize ATP. 

Dehydrogenase- the enzyme that removes hydrogen from an organic molecule.  Requires a coenzyme, NAD+.

Intermediates- Compounds that form between the initial reactant and the final product.

Glycolysis- the multistep chemical breakdown of a molecule of glucose into two molecules of pyruvate.

Chemiosmosis- The energy coupling mechanism.  The production of ATP using the energy of hydrogen ion gradients across membranes to phosphorylate ADP.

Substrate Level Phosphorylation- This is a form of ATP synthesis that occurs when when an enzyme transfers a phosphate group from a substrate molecule to ADP.

Redox Reaction- The movement of electrons from one molecule to another.  Oxidation reduction reaction.

Lactic Acid Fermentation- A process  by which muscle cells, some other cells, and certain bacteria generate NAD+.  NADH is oxidized to NAD+ as pyruvate is reduced to lactate.  

Diagram: This shows cellular respiration which is the set of the metabolic reactions and processes that take place in organism's cells to convert energy from nutrients into ATP, and then release waste products. The reactions involved in respiration are catabolic reactions that involve the oxidation of one molecule and the reduction of another. Respiration is one of the key ways a cell gains useful energy to fuel cellular reformations.

Relevant Video:
http://www.youtube.com/watch?v=vlZZUtpyCgQ


Summary: In this chapter, redox reactions, and the stages of fermentation and cellular respiration are covered.  The major steps of each of the processes , as well as the results are focused on.  Glycolysis, the Citric acid cycle, and oxidative phosphorylation are discussed in great detail.  

Chapter Two: The Chemical Basis of Life

Questions:

1. What are the differences between an ionic bond, and a covalent bond?
2. What makes a covalent bond polar? 
3. What are some of the benefits of radioactive isotopes?

Answers: 

1. In an ionic bond, the atoms are bound together by the attraction between oppositely-charged ions. For example, sodium and chloride form an ionic bond, to make NaCl, or table salt. In a covalent bond, the atoms are bound by shared electrons. 
2. A molecule is nonpolar when its covalently bonded atoms equally share electrons.  If a molecule is polar, electrons are not shared equally because there are differences in electronegativity.  An example of a polar molecule is water.  The H atoms of one water molecule may be attracted to O or N atoms. 
3. Radioisotopes can be used as radioactive tracers that follow molecules as they undergo changes in an organism.  They can also be used in the radiation treatment of cancer as well as in carbon dating.  

Important Facts:

1. The pH (potential of hydrogen) scale describes how acidic or basic a solution is.  It ranges from 0 to 14.  The lower a solution is on the scale, the more acidic it is.  Meaning that the higher a solution is, the more basic it is.  Every unit of the pH scale depicts a tenfold change in the concentration of hydrogen in a solution.
2. The different isotopes of an element possess different amount of neutrons, but still have the same amount of protons and electrons.  Some isotopes are stable because their nuclei don't have the tendency to lose neutrons.  Some isotopes, however, are radioactive or unstable.  This means that the isotope in question has a nucleus that decays spontaneously, giving off particles and energy.  Radioisotopes give off radiation that can be harmful to the health of an organism. 
3. Electron arrangement determines the properties of an atom.  The farther away an electron is from the nucleus, the greater its energy.  The number of electrons in the outermost shell determines the chemical properties.  The first electron shell can hold two electrons, while the second and third shell can have up to eight electrons.  Atoms whose outer electron shells are not full tend to participate in chemical reactions.
4. Hydrogen bonds are very important in life.  They make water molecules cohesive.  The cohesiveness of those molecules create surface tension and allow water to move from plant roots to leaves.  Cohesion creates surface tension.  Hydrogen bonds also cause water to be adhesive, meaning they cling to other substances.  
5. Hydrophilic substances are water-soluble.  Ionic compounds and polar molecules are hydrophilic.  Hydrophobic substances are not water soluble.  These substances include nonpolar molecules such as oils.    

Diagram: This shows the structure of an atom.  As you can see, the protons and neutrons make up the nucleus, while electrons surround them.  

Key Terms:

Matter- Anything that occupies space and has mass, composes living organisms.

Element- A substance that cannot be broken down to other substances by chemical reactions. (gold, copper,silver, iron)
Compound- A substance consisting of two or more different elements combined in a fixed ratio.
Trace Elements- The 25 elements essential to life.
Atom- The smallest unit of matter that still retains the properties of an element.
Proton- Subatomic particle that has a single positive charge.
Neutron- Subatomic particle that is electrically neutral.
Electron- Subatomic particle that has a single negative charge.
Cohesion- the tendency of molecules to stick together.
Adhesion- the clinging of one substance to another.
Electronegativity- An atom's attraction for shared electrons.
Solution- A liquid consisting of a uniform mixture of two or more substances.
Aqueous Solution- A solution in which water is the solvent.

Relevant Video: 

http://www.youtube.com/watch?v=K5Ks2X5TphI

Summary: 


This chapter focuses on the composition of matter and then delves  into the life-supporting properties of water.  It begins by discussing the 25 elements essential to the survival of living organisms.  The four most important ones are nitrogen, oxygen, carbon, and hydrogen.  The chapter goes on to explain how elements bond to form compounds.  There are two different types of chemical bonds, ionic bonds and covalent bonds.  It also explains what makes a molecule polar and what makes hydrogen bonds so important.  It also discusses the pH scale and the nature of solutions, solutes, and solvents.

Chapter Three: The Molecules of the Cells

 Questions: 

1. What are the seven functional groups?
2. Why does carbon create some of the most diverse and complex molecules?
3. What are the four types of macromolecules?  

Answers: 

1. The five functional groups are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl group.  The hydroxyl group is a hydrogen atom bonded to a on oxygen atom and it can form water molecules thus helping to dissolve organic compounds such as sugars.  It is polar.  The carbonyl group consists of carbon joined to oxygen with a double bond.  Its functional properties vary based on its structure and it is often found in sugars.  The carboxyl group is an oxygen atom double bonded to a carbon atom that is bonded to a hydroxyl group.  It has acidic properties.  The amino group consists of nitrogen bonded to two hydrogen atoms and to the carbon skeleton.  This group acts as a base.  The sulfhydryl group is made up of a sulfur atom bonded to an atom of hydrogen atom.  When two of these groups react and form a covalent bond they stabilize protein structure.  The phosphate group is a phosphorus  atom bonded to four oxygen atoms.  It has the potential to react with water thus releasing energy.  The methyl group consists of carbon bonded to three hydrogen atoms.  This group can affect the expression of genes.  
2. Carbon has four valence electrons meaning that it can form up to four covalent bonds.  These bonds can be single, double, or triple covalent bonds.  This means that it can form really large molecules whether they are chains, ring-shaped or branched meaning that carbon compounds can have many different isomers.    
3. The four different types of macromolecules are carbohydrates, lipids, proteins and nucleic acids.  Carbohydrates serve as fuel and building material.  Lipids are hydrophobic molecules that provide energy.  Proteins are polymers made up of amino acid monomers and have a variety of different functions.  Nucleic acids store and transmit hereditary information.  

Important Facts:

1. A protein consists of one or more polypeptide chains folded into a distinctive shape.  This determines the proteins function.  The primary structure of the protein is a polypeptide chain.  The secondary structure is the coiling/folding of the chain.  Tertiary structure is a three dimensional shape of a polypeptide,  while the quaternary structure is made up of more than one polypeptide.  
2. DNA and RNA are the two nucleic acids or nucleotides.  They are made up of a nitrogenous base (adenine, thymine, cytosine, guanine, uracil), a pentose (deoxyribose-DNA, ribose-RNA), and a phosphate group.
3. Denaturation occurs when a protein loses its shape and ability to function because of heat, a change in pH etc. 
4. Structural support polysaccharides are cellulose and chitin.  Cellulose is a major component in cell walls.  Chitin is commonly found in the exoskeleton of lobsters and insects.  Some energy storage polysaccharides are starch and glycogen.  Starch is often found in plants and stores substances.  Glycogen is used as storage in in animals.
5. A carbon skeleton is the chain of carbon atoms in an organic molecule.  They can be unbranched or branched and can contain double bonds.  This means that they can form many different isomers.  

Summary: This chapter focuses on organic compounds and the importance of carbon in life.  It talks about the hydrophilic functional groups.  The chapter also explains polymers and how they can be created by dehydration reactions as well as separated by hydrolysis.  The chapter then focuses on the structure and function of the organic macromolecules essential to living things: carbohydrates, lipids, proteins, and nucleic acids.

Diagram: This shows glucose and fructose forming sucrose through a dehydration reaction.  A molecule of water is released in order for the monosaccharides to bond.  

Key Terms:  
Hydrocarbons- Compounds made of only carbon and hydrogen atoms (methane, butane).
Polymers- smaller molecules bonded into chains.
Dehydration Reaction- a reaction that removes a molecule of water in order to link monomers together to form polymers.
Hydrolysis- The reverse of a dehydration reaction.  The bonds between monomers are broken by adding water to them.
Monosaccharides- carbohydrate monomers
Polysaccharides- carbohydrate polymers, long chains of sugar units
Unsaturated- fatty acids and fats with double bonds in the carbon chain.
Saturated- Fats with the maximum number of hydrogens.
Amino Acids- have an amino group and a carboxyl group and make up proteins.
Peptide Bond- amino acids joined together in a dehydration reaction.
Gene- distinct unit of inheritance



Relevant Video:
http://videos.howstuffworks.com/hsw/25354-compounds-organic-compounds-video.htm

Chapter Four: A Tour of the Cell

Questions:

1. What are the similarities and differences between the chloroplast and mitochondria?
2. What are three types of cell junctions found in animal tissues?  What are their functions?
3. What are some of the main differences and similarities between prokaryotic and eukaryotic cells?

Answers: 

1. The chloroplast is only found in the plant cell, while the mitochondria is found in both the animal and plant cell.  The chloroplast is the site of photosynthesis in the plant cell.  This means that it converses light energy from the sun into the chemical energy of sugar molecules.   The mitochondria carries out cellular respiration in the cell, using the energy from food to make ATP (adenosine triphosphate) that is essential for cellular work.  Both of these organelles have different structures that suit their particular function.  One similarity between these two organelles is the fact that they both evolved from being small prokaryotic cells that began living in other cells.     
2. Three types of cell junctions are tight junctions, anchoring junctions, and gap junctions.  Tight junctions are knit tightly together by proteins, preventing leakage of extracellular fluid across a layer of epithelial tissue.  Anchoring junctions are made up of filaments consisting of sturdy keratin proteins that keep these junctions glued to the cytoplasm.  They fasten the cells together into strong sheets.  Gap junctions work as channels that allow small molecules to flow through pores lined with proteins.  These pores allow for communication between neighboring cells. 
3. All cells have a plasma membrane, DNA, ribosomes and cytoplasm.  However, prokaryotic cells are much smaller than eukaryotic cells and are relatively simpler.  They don't even have a membrane bound nucleus.  The eukaryotic cell is much more complex.  Not only does it have a membrane bound nucleus, but it also only has a membrane.  The prokaryotic cell has a cell wall that protects it from its environment.  

Important Facts: 

1. Eukaryotic cells are separated into four different functional compartments.  They are manufacturing, breakdown of molecules, energy processing, and structural support, movement and communication.  Manufacturing involves the nucleus, ribosomes, the golgi apparatus, and the endoplasmic reticulum.  Breakdown of molecules involves peroxisomes, lysosomes, and vacuoles.  Energy processing involves the mitochondria in animal cells, and the chloroplast in plant cells.  Structural support, movement and communication involve the cytoskeleton, plasma membrane, and cell wall.   
2. The endoplasmic reticulum (ER) is a network of membranes and sacs.  It makes up much of the cell.  There are two types of ER: the smooth ER and the rough ER.  The smooth ER has three main functions.  These include the synthesis of lipids, metabolism of carbohydrates, and the detoxification of drugs and poisons.  The rough ER is called rough because it has ribosomes on its structure.  These ribosomes synthesize proteins.  Then the polypeptide chains travel across the ER membrane.
3. Endosymbiosis suggests that the mitochondria and chloroplast were small prokaryotes before they began growing in larger cells.  This hypothesis was proposed because both organelles contain DNA and ribosomes.  The DNA has a similar structure to the DNA found in prokaryotes.  Also the ribosomes are more similar to those found in prokaryotes rather than the ones found in eukaryotes.   
4. The extracellular matrix helps hold cells together and protects the plasma membrane.  It is mainly made up of glycoproteins that form strong collagen fibers outside the cell.  These fibers are connected to a network of other types of glycoproteins.  These glycoproteins connect to a polysaccharide molecule.  The ECM attaches to the cell through other glycoproteins that bind to integrins (membrane proteins).  Integrins transmit information between the ECM and the cytoskeleton.  
5. The light microscope can magnify living and dead cells up to 1,000 times.  The ultrastructure of cells can be revealed by scanning and transmission electron microscopes which have greater resolution and magnification.  

Diagram:  This diagram shows the structure of the plasma membrane as well as where it lies in relation to the entire cell.  It shows what the plasma membrane is composed of in great detail. 

Key Terms: 

Endomembrane System- The system of membranes within a cell that includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane.

Lysosomes- Sacs of hydrolytic enzymes that can digest large molecules (proteins, polysaccharides, fats, nucleic acids)  and recycle them into the cell. 
Plasma Membrane- Forms the boundary of a cell and selectively permits the passage of materials into and out of the cell.  Its structure is made up of phospholipids, proteins, and carbohydrates.
Nucleus- Contains most of DNA essential for the cell and makes mRNA that will later produce proteins.  It is the control center of the cell.
Ribosomes- Sites of protein synthesis in the cell.
Golgi Apparatus- The postal system of the cell.  Here, proteins are modified, stored, and shipped.
Cytoskeleton- Network of protein fibers that run throughout the cytoplasm.  It is responsible for support, motility, and regulating biochemical activities.
Central Vacuoles- Store and breakdown some waste products.  Take up 80% of the plant cell.
Cell Wall- Plant cells only.  Helps maintain the shape of the cell.  Mainly made of cellulose.
Plasmodesmata- Channels that penetrate adjacent plant cell walls and allow the passage of some molecules from cell to cell.
Peroxisomes- Single membrane bound structures in the cell.  They are responsible for various metabolic functions that involve the production of hydrogen peroxide and break down fatty acids that are then sent to the mitochondria for fuel.

Summary: This chapter focuses on the differences between prokaryotic cells and eukaryotic cells.  It also deals with the different organelles and where they lie in the four key functional groups of a cell: manufacturing, breakdown, energy processing, and communication between cells.  The chapter goes into detail describing the structure and function of each organelle and why they are important to the cell.

Relevant Video: 
http://www.youtube.com/watch?v=Hmwvj9X4GNY&feature=related  

Chapter Five: The Working Cell

Questions:

1. What is an exergonic reaction?  What is an endergonic reaction? What are their differences?
2. Why is selective permeability important to the plasma membrane?
3. What are the differences between an isotonic solution, a hypertonic solution, and a hypotonic solution?

Answers:

1. An exergonic reaction is a chemical reaction that releases energy.  This means that it begins with reactants whose covalent bonds possess more energy than those in the products.  In this kind of reaction, an amount of energy equal to the difference in potential energy between the reactants and the products is released to the surrounding atmosphere.  An example of this reaction is the burning of wood.  As it burns, the wood releases heat and light.  An endergonic reaction requires an input of energy in order to take place.  This means that their products are high in potential energy.  However, the reactants have little and must absorb energy from their surroundings.  This is potential energy that is stored in the covalent bonds of the product molecules.  
2. Selective permeability is important because it allows some substances to cross the plasma membrane more easily than others.  This helps to keep the cells functioning properly because it gives the cell control of what enters the cell.  
3. In an isotonic solution there is no net movement of water across the plasma membrane because water moves at the same rate in both directions.  In a hypertonic solution the cell will lose water to its surroundings.  This means that their are more solutes in the water around the cell so the water moves to the higher concentration of solutes.  And so, since the cell loses water to the environment, it will shrivel and may die.  In a hypotonic solution water enters the cell faster than it leaves because there are fewer solutes in the water around the cell.  So the water outside the cell moves into the cell where there is a higher concentration of solutes.  Because of this the cell will swell and may rupture.  

Important Facts: 

1. Membranes are made up of proteins and phospholipids and are often described as fluid mosaics.  The surface appears mosaic because of the proteins embedded in the phospholipids.  The proteins roam around on the phospholipids making the membrane fluid.  Most phospholipids are made from unsaturated fatty acids that have kinks in their tails which makes it so that they cannot be packed together tightly.  This tendency keeps them fluid.   
2. In active transport, substances are moved against their concentration gradient using energy in the form of ATP.  An example of active transport is the sodium-potassium pump,  a transmembrane protein that pumps sodium out of the cell while pumping potassium in.  In passive transport, substances are diffused across the cell membrane without requiring any energy whatsoever.  
3. Diffusion is the process in which particles move from an area of more concentrated particles to an area where they are less concentrated.  The particles diffuse down their concentration gradient until they reach equilibrium.  
4. Environmental conditions, including temperature and pH, influence enzyme activity.  For example, human enzymes function best at 37 degrees Celsius (body temperature).  If temperature is too high, enzymes will denature, rendering them useless because the function of an enzyme is directly connected to its structure.  If the structure changes, the enzyme can not perform its function.   
5. The path of proteins begins in the nucleus.  mRNA is transcribed from DNA and then travels out of the nucleus into the cytoplasm until they reach the ribosomes.  Some of these ribosomes are connected with the rough endoplasmic reticulum where the mRNA are translated into proteins.  The proteins then carry out their metabolic function in the cell.  Some act as enzymes, others as structural components etc. 

Diagram: This shows an enzyme catalyzing a cellular reaction.  You can see the substrate (the specific reactant that an enzyme acts on) bind to the enzyme's active site.  Then the products are released and the enzyme is free to bind once again.

Key Terms:
Tonicity- describes the ability of a solution to cause a cell to gain or lose water.
Isotonic- indicates that the concentration of a solute is the same on both sides.
Facilitated Diffusion- A type of passive transport that does not require energy.  Aquaporins are required.
Exocytosis- used to export bulky molecules (proteins, polysaccharides)
Endocytosis- used to import substances useful to the livelihood of the cell.
Phagocytosis- engulfment of a particle by wrapping cell membrane around it, forming a vacuole.
Chemical Energy- potential energy because of its energy available for release in a chemical reaction.
Thermodynamics- the study of energy.  First law- energy is constant.  Second law- energy conversions increase the disorder of the universe.  (Entropy- measure of disorder)
Exergonic Reaction- A chemical reaction that releases energy in covalent bonds of the reactions.
Endergonic Reaction- A chemical reaction that requires energy and yields products rich in potential energy.
Metabolism- the combination of an organism's exergonic and endergonic reactions.
Metabolic Pathway- A series of chemical reactions that either break down or build a complex molecule.
ATP- Adenosine triphosphate, renewable source of energy for the cell.

Summary: This chapter is mainly about the structure and function of the plasma membrane.  It describes many of the important processes such as diffusion, passive transport and active transport.  It also talks about hypotonic, hypertonic, and isotonic solutions as well as exocytosis and endocytosis.  The chapter then goes on to explain the role of energy in the cell as well as the main types of chemical reactions.  Before the chapter ends, it also describes how enzymes function, both as catalysts and as inhibitors.

Video on Diffusion and Osmosis:
http://www.youtube.com/watch?v=aubZU0iWtgI&feature=fvw

Chapter One: Themes in the Study of Biology

Questions:

1. What are the properties common to all organisms?
2. What separates Domain Bacteria from Domain Archaea? What makes them similar?
3. How does the process of Natural Selection work?

Answers:

1. Animals, despite their vast differences, are similar in many ways.  Some properties that all animals possess include order, regulation, growth and development, energy processing, response to the environment, reproduction, and evolutionary adaptation, all of which are very important to their survival.  Order means that all animals show complex organization.  Regulation is important because, though the environment can change at any given time, an animal can keep its internal environment within limits that sustain life.  The important thing about growth and development is that heredity dictates its pattern in an organism.  Energy processing refers to the tendency of organisms to take in energy and transform it to perform all of life's activities.  Response to the environment concerns all organisms because every one responds to environmental stimuli.  All organisms also participate in the reproduction of their own kind.  Evolutionary adaptation refers to the changes that evolve over many generations as animals with the best traits pass them to their offspring.
2. Domain Bacteria and Domain Archaea are both made up of prokaryotes.  For a time they were combined into the same kingdom, but new evidence regarding DNA and other molecules suggests that they are completely different branches of life.
3. Natural selection is a mechanism by which populations adapt and evolve.  The individual organisms who happen to be best suited to an environment survive and reproduce most successfully, producing many similarly well-adapted descendants. After numerous such breeding cycles, the better-adapted dominate. 

Important Facts:
1. The levels of biological organization goes as follows: Biosphere, ecosystem, community, population, organism, organ, tissue, cell, organelle, molecule, and finally the atom.  Each level greatly affects the following level, just as it is substantially affected by its preceding levels. Each part helps define the emergent properties of its whole.
2.  In an ecosystem, chemical nutrients participate in an essential cycle.  They are passed from the atmosphere and the soil to producers to consumers to decomposers and then back to the environment. Energy only flows through an ecosystem once.  It passes from the sun to producers then to consumers and exits as heat.
3. The basic unit of life is the cell which performs all the necessary duties required for life.  Eukaryotic cells are enclosed in a membrane and contain a DNA-containing nucleus.  Prokaryotes lack the afore mentioned organelles and are much smaller.
4.  DNA is the genetic information that programs all inherited traits and the production of an organism's molecules.  All genes are coded in sequences that always contain the same four building blocks.
5.  There are different names and classifications for every species.  Some are classified under Domain Bacteria or the Domain Archaea, both of which include only prokaryotic cells.  The rest are classified under Domain Eukarya, which includes only eukaryotic cells.  Various different protist kingdoms emerge from this domain.  They are the kingdoms Fungi, Bacteria, and Animalia.
6. Natural selection is best defined as an editing mechanism that occurs when populations of organisms with inherited variations, having been exposed to environmental factors that favor them over others, have more reproductive success and so pass their genes on to their descendants.

Diagram-  This focuses on the cycling of chemical nutrients and flow of energy in an ecosystem. 

Summary: Chapter one focuses on life's hierarchy of organization.  It talks about the cycling of nutrients and flow of energy in an ecosystem as well as the cell.  It discusses DNA and its importance to life as well as the three domains of organisms.  The chapter also covers the theories of evolution and natural selection and how they're important to life.  It then includes the processes of science.

Key Terms
Biosphere-All  the environment on Earth that supports life.
Ecosystem-All the organisms living in a particular area, including the nonliving components of the environment.  (water, air, soil etc.)
Community- The entire range of organisms living in an ecosystem.
Population- Consists of all the individuals of a species living in a specified area. EX: lions inhabiting a savannah.
Organism- An individual living thing.
Organ System- Consists of several organs working together in performing specific functions.  EX: digestive system, nervous system etc.
Tissues- Make up organs.  Several different types, each with a specific function and made up of similar cells.
Organelle- A membrane bound structure that performs a specific function in a cell.
Molecule- A cluster of atoms held together by chemical bonds.
Prokaryotic cell- Simpler, and usually smaller than a eukaryotic cell.  Make up microorganisms called bacteria. 
Eukaryotic cell- Makes up forms of life such as animals, plants, and fungi.  It is subdivided by internal membranes into many different functional compartments or organelles.


Video:  
http://www.youtube.com/watch?v=GcjgWov7mTM