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