Chapter 6: How Cells Harvest Chemical Energy

Three questions about the chapter:
1. What are the types of fibers all human muscles contain?
   All human muscles contain slow and fast fibers, but muscles differ int he percentage of each.
2. What are the three main stages of cellular respiration?
    The three main stages of cellular respiration are: glycolysis, the citric acid cycle, and the oxidative phosphorylation.
3. What is the movement of electrons from one molecule to another called?
   It is called oxidation-reduction reaction, or redox reaction.

Five main factors from the reading:
1. Photosynthesis and cellular respiraton provide energy for life.
2. Cellular respiration banks energy in ATP molecules.
3. The human body uses energy from ATP for all its activities.
4. Glycolysis harvests chemical energy by oxidizing glucose to pyruvate.
5. Pyruvate is chemically groomed for the citric acid cycle.

Diagram:

    
In cellular respiration, electrons fall down an energy staircase and finally reduce oxygen. Electron transport chain also controls the release of energy for synthesis of ATP.









Link: http://www-3.unipv.it/webbio/anatcomp/freitas/2008-2009/biocell_BT08-09.htm


Summary:
    The introduction section of the chapter talks about the difference between a marathoner and a sprinter. It says that the main difference between these two is that the sprinters have more fast fibers, and the marathoners have more more slow fibers. The introduction also gives us a brief definition of cellular respiration - the aerobic harvesting of energy from sugar by muscle cells or other cells. 
    Photosynthesis and cellular respiration provide energy for life. Breathing supplies oxygen to our cells for use in cellular respiration and removes carbon dioxide. When we breathe we take in oxygen and breathe out less oxygen and more carbon dioxide. The oxygen helps our cells work properly. Cellular respiration banks energy in ATP molecules. Glucose and oxygen combine together and produce carbon dioxide, water and ATP. The human body uses energy from ATP for all its activities. Energy units are called kilocalories (kcal). Cells tap energy from electrons "falling" from organic fuels to oxygen. The movement of electrons from one molecule to another is an oxidation-reduction reaction, or redox reaction for short. In a redox reaction, the loss of electrons from one substance is called oxidation, and the addition of electrons to another substance is called reduction. Two key players in the process of oxidizing glucose are an enzyme called dehydrogenase  and a co-enzyme called NAD+. In cellular respiration, electrons fall down an energy staircase and finally reduce oxygen. This is called electron transport chain. Cellular respiration occurs in three main stages: glycolysis, the citric acid cycle and oxidative phosphorylation. Glycolysis harvests chemical energy by oxidizing glucose to pyruvate. This happens in substrate-level phosphorylation where an enzyme transfers a phosphate group from a substrate molecule directly to ADP, forming ATP. This process produces a small amount of ATP in both glycolysis and the citric acid cycle. Pyruvate is chemically groomed for the citric acid cycle. The citric acid cycle completes the oxidation of organic molecules, generating many NADH and FADH2 molecules. Most production of ATp occurs by oxidative phosphorylation though, and glycolysis and the citric acid cycle's mission is the help this. The last step of the oxidative phosphorylation ATP synthases. In chemiosmosis, the potential energy of H+ concentration gradient is used to make ATP. The concentration gradient drives the diffusion of H+ through ATP synthases, protein complexes built into the inner membrane that synthesize ATP. Certain poisons though might interrupt critical events in cellular respiration. Some of them are rotenone, cyanide, carbon monoxide, DNP, and oligomycin. Each molecule of glucose yields many molecules of ATP. Fermentation enables cells to produce ATP without oxygen. Our muscle cells, a few other cell types, and certain bacteria can regenerate NAD+ by a process called lactic acid fermentation. Another type of fermentation is the alcohol fermentation, used in brewing, wine making, and baking. Glycolysis evolved early in the history of life on Earth. Ancient prokaryotes probably used it to make ATP long before oxygen was present in Earth's atmosphere. Cells use many kinds of organic molecules as fuel for cellular respiration, which means that eating certain kinds of food yields ATP to our body. Food molecules provide raw materials for biosynthesis.
 
Key Terms:
1.  Redox reaction - the movement of electrons from one molecule to another.
2. Oxidation - the loss of electrons from one substance.
3. Reduction - the addition of electrons to another substance.
4. Electron transport chain - controls the release of energy for synthesis of ATP, and it helps electrons move.
5. Substrate-level phosphorylation - an enzyme transfers a phosphate group from a substrate molecule directly to ADP, forming ATP.
6. Intermediates - the compounds that form between the initial reactant, glucose, and the final product, pyruvate.
7.  Lactic acid fermentation - a process by which muscle cells, a few other cell types, and certain bacteria can regenerate NAD+.
8.  Facultative anaerobe - can make Atp either by fermentation or by oxidative phospohorylation, depending on whether oxygen is available.
9.  NAD+ - nicotinamide adenine dinucleotide is an organic molecule that cells make from the vitamin niacin and use to shuttle electrons in redox reactions.
10. Dehydrogenase - a key enzyme in the process of oxidizing glucose.

Chapter 5: The Working Cell

Three questions about the chapter:
1. What is the difference between passive and active transport?
   Passive transport is diffusion across a membrane with no energy investment, while active transport requires energy.
2. What are the three types of solutions?
   The three types of solutions are isotonic, hypotonic and hypertonic.
3. What is the first law of thermodynamics?
   According to the first law of thermodynamics, the energy in the universe is constant. 


Five main facts from the reading:


1. Transport proteins may facilitate diffusion across membranes.
2. Exocytosis and endocytosis transport large molecules across membranes.
3. Cells transform energy as they perform work.
4. Energy cannot be created or destroyed, it can only be transferred.
5. Chemical reactions either release or store energy.


Diagram:

This diagram shows different passive transport of molecules. The first row shows a solution separated from pure water by a membrane. The second row illustrates the important point that two or more substances diffuse independently of each other.










Link: http://teacherwanafizah.blogspot.com/2009/03/biology-passive-transport-and-active.html








Summary:


   The introduction talks about some sea animals who have the ability to become invisible and protect themselves or hunt. They do this by turning on some lights, by chemical reactions.
   The next section of the chapter taught us that membranes are fluid mosaic of phospholipids and proteins. They exhibit selective permeability, which is, they allow some substances to cross more easily than others. Membranes form spontaneously, a critical step in the origin of life. Passive transport is diffusion across a membrane with no energy investment. Diffusion is the tendency for particles of any kind to spread out evenly in an available space, moving from where they are more concentrated to regions where they are less concentrated. Osmosis is the diffusion of water across a membrane. Water balance between cells and their surroundings is crucial to organisms. The term tonicity describes the ability of a solution to cause a cell to gain or lose water. The three types of solutions are: isotonic, hypotonic, and hypertonic. The control of water balance is called osmoregulation. Transport proteins may facilitate diffusion across membranes. When a protein makes it possible for a substance to move down its concentration gradient, the process is called facilitated diffusion. Cells expend energy in the active transport of a solute against its concentration gradient. In active transport a cell must expend energy to move a solute against its concentration gradient - that is, across a membrane toward the side where the solute is more concentrated. The cell's energy molecule ATP supplies the energy for most active transport. Exocytosis and endocytosis transport large molecules across membranes. Cells transform energy as they perform work. They are three kinds of energy: kinetic energy, potential energy, and chemical energy. There also two laws, which govern energy transformations: the first and the second laws of thermodynamics. Thermodynamics is the study of energy transformations that occur in a collection of matter. Chemical reactions either release or store energy. An exergonic reaction is a chemical reaction that releases energy. ATP shuttles chemical energy and drives cellular work.


Key Terms:


1. Passive transport - diffusion across a membrane with no energy investment.
2. Osmosis - the diffusion of water across a membrane.
3. Active transport - a cell must expend energy to move a solute against its concentration gradient.
4. Endocytosis - a transport process that is the opposite of exocytosis.
5. Exocytosis - a cell uses the process of exocytosis to export bulky materials such as proteins or polysaccharide. 
6. Phagocytosis - cellular eating.
7. Pinocytosis - cellular drinking.
8. Energy - the capacity to perform work.
9. Kinetic energy - the energy of motion.
10. Chemical energy - a term that refers to the potential energy available for release in a chemical reaction.

Chapter 4: A Tour of the Cell

Three questions about the chapter:
  1. What are the two main types of microscopes?
   The two main types of microscopes are light and electron microscope.
   2. What are the two main types of cells?
   The two main types of cells are prokaryotic and eukaryotic cells.
   3. What is the function of the mitochondria?
   Its function is to produce energy.


Five main facts from the reading:
   
   1. Eukaryotic cells are bigger and more complex than prokaryotic cells.
   2. The nucleus is the cell's genetic control center.
   3. The endoplasmic reticulum is a biosynthetic factory.
   4. Lysosomes are digestive compartments within a cell.
   5. Chloroplasts convert solar energy to chemical energy.


Diagram:

This diagram shows the main differences between the prokaryotic and the eukaryotic cells. We can see that the eukaryotic is bigger, more complex, and has more organelles than the prokaryotic.
























Link: https://www.etap.org/demo/biology1/instruction3tutor.html


Summary:
    The introduction of the chapter talks about the moving of cells.  We can see the little cells and their move through microscopes and micrographs (pictures taken through microscopes). We know that almost all cells move, and some of them move with an incredible speed.
    The next section of the chapter taught us that microscopes reveal the world of the cell. There two main different types of microscopes: light microscope (LM) and electron microscope (EM). There two types of electron microscope: the scanning electron microscope (SEM) and the transmission electron microscope (TEM).  With the microscope we can examine the different types of cells. Most of the cells are microscopic (very small). They are two different types of cells: prokaryotic cells and eukaryotic cells. Prokaryotic cells are smaller and structurally simpler than eukaryotic cells. Both types of cells have plasma membrane, chromosomes, cytoplasm, DNA, and ribosomes. Eukaryotic cells are partitioned into functional compartments. They also have various organelles in the cytoplasm. Many of the chemical activities of cells, activities known collectively as cellular metabolism, occur within organelles. The structure of membranes correlates with their functions. The nucleus is the cell's genetic control center. It contains most of the cell's DNA and controls the cell's activities by directing protein synthesis. Eukaryotic chromosomes are made up of a material called chromatin, which is a complex of proteins and DNA. Ribosomes make proteins for use in the cell and export. Free ribosomes are suspended in the fluid of the cytoplasm, while bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope. Many cell organelles are connected through the endomembrane system. An extensive network of flattened sacs and tubules called the endoplasmic reticulum is the prime example of the direct interrelatedness of parts of the endomembrane system. 
   The endoplasmic reticulum is a biosynthetic factory. There are two types of endoplasmic reticulum: smooth, called like this, because it lacks attached ribosomes, and rough, which has ribosomes that stud the outer surface of the membrane. Some of the other organelles and their functions are: the Golgi apparatus, which finishes, sorts, and ships cell products. Lysosomes are digestive compartments within a cell. Vacuoles function in the general maintenance of the cell. Mitochondria harvest chemical energy from food. Chloroplasts convert solar energy to chemical energy. 
   The cell's internal skeleton helps organize its structure and activities. The network of protein fibers is called cytoskeleton. There are three main types of fibers of the cytoskeleton: microfilaments, intermediate filaments, and microtubules. Cilia and flagella move when microtubules bend. Problems with sperm motility may be environmental or genetic.
   There are three types of cell junctions that are found in animal tissues: tight junctions, which prevent leakage of extracellular fluid across a layer of epithelial cells, anchoring junctions, which are fastened cells together into strong sheets, and gap junctions, which are channels that allow small molecules to flow though protein-lined pores between neighboring cells.
Key Terms:
1. Chromosomes - they cary genes made of DNA.
2. Ribosomes - tine structure that make proteins according to instructions from the genes.
3. Cytoplasm - the entire region between the nucleus and the plasma membrane.
4. Nucleoid - the region where the DNA of a prokaryotic cell is coiled into.
5. Organelles - little organs in the cytoplasm in eukaryotic cells.
6. Nucleus - contains most of the cell's DNA and controls the cell's activities by directing protein synthesis.
7. Nuclear envelope - a double membrane perforated with protein-lined pores that control the flow of materials into and out of the nucleus.
8. Lysosomes - the digestive compartments within a cell.
9. Peroxisome - an organelle that is not part of the endomembrane system but is involved in various metabolic functions.
10. Mitochondria - organelles that carry out cellular respiration in nearly all eukaryotic cells, converting the chemical energy of foods such as sugars to the chemical energy of a molecule called ATP.

Chapter 3: The Molecules of Cells

Three questions about the chapter:
   1. What are the functional groups of organic compounds?
  They are hydroxyl group, carbonyl group, carboxyl group, amino group, phosphate group and methyl group.
   2. How can we recognize a phosphate group?
  We can do this by seeing the phosphate element into the example, expressed by (P)
   3. How can we recognize a carbonyl group?
  We can do this by seeing the double bond connection between the carbon (C) and the oxygen (O) in the example.
   4. How can we recognize an amino group?
  We can do this by seeing the single bond connection between the nitrogen (N) and the two hydrogens (H) in the example.
   5. What are polymers made of?
  Polymers are made of connected monomers. Poly means many, and mono means single.


Five main facts from the reading:
   1. Carbon - based molecules are called organic compounds.
   2. The variations in carbon skeletons are: length, branching, double bonds, and rings.
   3. Two monomers are connected by a reaction, called dehydration.
   4. Two monomers are broken down by a reaction, called hydrolysis.
   5. The four levels of protein structure are: primary, secondary, tertiary, and quaternary structure.


Diagram: 

This diagram shows the specific elements and connections of each of the functional groups of organic compounds and helps us recognize the different groups.


























Link: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/H.html

Summary:
  The introductory section of this chapter talks about lactose.  Milk and other dairy products have long been recognized as highly nutritious foods, rich in protein and minerals necessary for healthy teeth and strong bones. For many people though these health benefits come with a digestive discomfort. Such people suffer from lactose intolerance, or the inability to properly break down lactose, the main sugar found in milk.
   After this the chapter talks about the life's molecular diversity, which is based on the properties of carbon. Carbon-based molecules are called organic compounds. Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons. The chain of carbon atoms in an organic molecule is called a carbon skeleton. The different variations of carbon skeleton are: length, branching, double bonds, and rings. Compounds with the same formula, but different structures are called isomers. The next section of the chapter talks about the characteristic chemical groups, which help determine the properties of organic compounds. A hydroxyl group is consisted of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to the carbon skeleton. In a carbonyl group, a carbon atom is linked by a double bond to an oxygen atom. A carboxyl group is consisted of a carbon double-bonded to an oxygen and also bonded to a hydroxyl group. An amino group is composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton. A phosphate group is consisted of a phosphorus atom bonded to four oxygen atoms. A methyl group is consisted of a carbon bonded to three hydrogens.
   The next section of the chapter talks about that cells make a huge number of large molecules from a small set of small molecules. Two monomers can be connected to one polymer by a dehydration reaction. During this reaction water is being released. One polymer can be broken down to two monomers by hydrolysis reaction. This reaction needs water to be successful. Monosaccharides are the simplest carbohydrates. The name carbohydrate refers to a class of molecules ranging from the small sugar molecules dissolved in soft drinks to large polysaccharides, such as the starch molecules we consume in pasta and potatoes. The carbohydrate monomers are monosaccharides. Cells link two single sugars to form disaccharides. We also learned about the high-fructose corn syrup and how unhealthy it is for us. After this the chapter talked about polysaccharides, which are long chains of sugar units. Then we learned that fats are lipids that are mostly energy-storage molecules. Lipids are divers compounds that are grouped together because they share one trait -  they mix poorly, if at all, with water. Lipids are hydrophobic, or in other words they do not like water. Phospholipids and steroids are important lipids with a variety of functions. Cells could not exist without phospholipids. The chapter also taught us that anabolic steroids pose health risks, and most of them are illegal, so it is better for us to stay away from them. Proteins, on the other side, are essential to the structures and functions of life. A protein is a polymer constructed from amino acid monomers. Proteins are made from amino acids linked by peptide bonds. Amino acids all have an amino group and a carboxyl group.  A protein's specific shape determines its function. A protein's shape depends on four levels of structure: primary, secondary, tertiary, and quaternary. We also learned that Linus Pauling contributed to our understanding of the chemistry of life. The last two things chapter talked about were the nucleic acids, which are information-rich polymers of nucleotides, and lactose tolerance, which is a recent event in human evolution.


Key Terms:
 1. Carbon skeleton - the chain of carbon atoms in an organic molecule.
 2. Isomers - compounds with the same formula but different structures.
 3. Hydrophilic - water-loving,
 4. Enzymes - specialized macromolecules that speed up chemical reactions in cells.
 5. Monosaccharides - the carbohydrate monomers.
 6. Fat - a large lipid made from two kinds of smaller molecules: glycerol and fatty acids.
 7. Saturated - fats with the maximum number of hydrogens.
 8. Unsaturated - fatty acids and fats with double bonds in the carbon chain.
 9. Anabolic steroids - synthetic variants of the male hormone testosterone.
10. Steroids - lipids whose carbon skeleton contains four fused rings.

Chapter 2: The Chemical Basis of Life

Three questions about the chapter:


   1. Are radioactive isotopes helpful or harmless?
     Radioactive can be helpful but also very dangerous for us. They are used in medicine to diagnose different sicknesses, but they can damage our molecules, especially our DNA.
   2. Why a water strider can walk on water without sinking?
     The water has cohesion and adhesion. These two help water to be able to hold very little object on its surface.
   3. Why does ice stay on top of water?
   Ice stays on top of water because of it is less dense than the liquid water. The hydrogen bonds in ice are stable, but the ones in water constantly break up and re-form.


Five main facts from the reading:


  1.  The four main elements found in humans are oxygen, carbon, nitrogen, and hydrogen. They make 96.3% of the human body weight.
  2.  Trace elements are elements found in the human body, but only in minute quantities. They are calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium.
  3.  Iron is needed by the human body, so it might be found in some food, such as some cereals.
  4.  Atoms can be joined into molecules through covalent, ionic, or hydrogen bonds.
  5.  Heat and temperature are two different things. The first one is the amount of energy associated with the movement of atoms and molecules in a body of matter. The second one measured the intensity of hear - that is, the average speed of molecules rather than the total amount of heat energy in a body of matter.


Diagram:

Link:http://www.gather.com/viewImage.action?fileId=3096224745391211


This diagram represents an atom. The white empty circles are the neutrons. The circles with positive signs inside are the protons. And the little circles with the negative signs are the electrons. The protons and neutrons are located in the nucleus of the atom.




Summary:


    The introduction page of this chapter talks about the so called "devil's gardens" and the special kind of ants living in there. These ants prevent the growing of many kinds of plants by injecting intruders with a poisonous chemical.
    The first main things we learned about in this chapter were the elements, atoms and molecules. We learned that matter is everything that occupies space and has mass. We learned that an element is a substance that cannot be broken down by chemical means, and that the four main elements in the human body are oxygen, hydrogen, nitrogen, and carbon. Trace elements are elements that our body needs to work properly. They do not make up much of our body, but we need them, so they are common additive to food and water. Elements can combine to form compounds. For example sodium and chlorine can be combined to produce sodium chloride or table salt. An atom is the smallest unit of matter that still retains the properties of an element. Atoms are consisted of protons, which have positive charge, neutrons, which do not have any charge, and electrons, which have negative charge. The protons and neutrons are located in the nucleus of the atom. Every element has an atomic number, which is represented by the numbers of protons. Every atom has a mass number, which is represented by the sum of protons and neutrons. Some elements have isotopes. An isotope is an element with same atomic number, but with different mass numbers. Some isotopes are radioactive. Radioactive isotopes can be helpful, but also harmless. 
    Electrons occur only at certain energy levels, called electron shells. Atoms join into molecules by chemical bonds. They are three different types of bonds Ionic bonds, where an electron from one atom goes to another atom, covalent, where electrons are shared by elements, and hydrogen, where atoms attracted based on their charge. The covalent bond is the strongest bond, and the hydrogen bond is the weakest one. The hydrogen bonds can be nonpolar covalent bonds and polar covalent bonds. An atom's attraction for shared electrons is called its electronegativity. After this we learned that ice is less dense than liquid water, because the molecules in the ice are stable, and the ones in the liquid water are constantly moving, breaking, and re-forming. We also learned that water os the solvent of life. A solution is a liquid consisting of a uniform mixture of two or more substances. After this we read about that the chemistry of life is sensitive to acidic and basic conditions. We use the pH scale to describe how acidic or basic a solution is. 
    The least few things we learned were that acid precipitation and ocean acidification threaten the environment. Acid precipitation refers to rain, snow, or fog with a pH lower than 5.6. The search for extraterrestrial life centers on the search for water. The last topic of the chapter was taught us that chemical reactions make and break bonds, changing the composition of matter.


Key Terms:


  1.Matter - anything that occupies space and has mass.
  2.Element - a substance that cannot be broken down to other substances by ordinary chemical means.
  3.Compound - a substance consisting of two or more different elements combined in a fixed ratio.
  4.Proton - a subatomic particle with a single positive electrical charge (+).
  5.Elecron - a subatomic particle with a single negative electrical charge (-).
  6.Atomic number - the number of protons in an element.
  7.Mass number - the sum of the protons and neutrons in an element's nucleus.
  8.Isotope - has the same number of protons and electrons and behaves identically in chemical reactions, but  has different number of neutrons.
  9.Adhesion - the clinging of one substance to another.
  10.Base - a compound that accepts hydrogen ions and removes them from solution.

Chapter 1: Biology, Exploring Life

Three questions about the chapter:

 

   1. What are the levels of life's hierarchy of organizations?

     The levels of life's hierarchy of organizations are: (from the smallest to the biggest one) molecule->organelle->cell->tissue->organ->organ system-> organism->population->community->ecosystem->biosphere.

   2. What are the two different kinds of cells in living things?

     The two different kinds of cells are prokaryotic and eukaryotic. The eukaryotic cells are bigger and more complex than the prokaryotic. They also contain nucleus, which the prokaryotic do not.

   3. Which two main approaches do scientists use to learn about nature?

     The two main approaches scientists use to learn about nature are discovery science, which contains inductive reasoning, and hypothesis-based science, which contains deductive reasoning.

Five main facts from the reading:

   1. Producers (plants) are the living things which provide food for a typical ecosystem, and consumers are the ones who eat the producers (people, animals).

   2. There are three domains of life: Archaea, Bacteria, and Eukarya. People are in the most developed domain - Eukarya.

   3. In every DNA chain, gene A combines with gene T, gene T combines with gene A, gene G combines with gene C, and gene C combines with gene G.

   4. All living things exhibit complex organization.

   5. Inherited information carried by genes controls the pattern of growth and development of organisms.

Diagram:

This diagram shows that the eukaryotic cell is bigger and more complex than the prokaryotic. Link:http://www.clipartof.com/interior_wall_decor/details/Biology-Diagram-Of-Prokaryotic-And-Eukaryotic-Cells-Poster-Art-Print-13964

Summary:  
   This chapter's introduction talks about how leopards are one of strongest climbing animals, and this is the reason why they eat their victims on trees, so nobody can reach them and steal their food.
   In the essence of the chapter we learned first about the themes in the study of Biology and the life's hierarchy of organization. We learned about the fact that living organisms interact with their environments, exchanging matter and energy by producers and consumers. We looked up briefly at prokaryotic and eukaryotic cells and we saw that eukaryotic cells are bigger and more complex. We learned about the unity of life, and that all forms of life have common features. We looked briefly at the three domains of living organisms: Bacteria, Archaea, and Eukarya. We learned about Charles Darwin and his most important book called "On the Origin of Species by Means of Natural Selection". We read about the two main approaches scientists use to learn about nature. We briefly learned about how biology, technology, and society are connected in important ways and how is evolution connected to our everyday lives.

Key terms:

   1. Molecule - a cluster of atoms held together by chemical bonds.

   2. Organelle - a membrane-bound structure that performs a specific function in a cell.

   3. Cell - separated from its environment by a boundary called a membrane.

   4. Tissue - many cells, organized into a communication network of spectacular complexity.

   5. Organ - a group of tissues that has a common purpose.

   6. Organ system - consists of several organs that work together.

   7. Organism - an individual living thing.

   8. Population - consists of all individuals of a species living in a specified area.

   9. Community - the entire array of organisms inhabiting a particular ecosystem.

   10. Ecosystem - consists all of the organisms living in a particular area.