Ch.3 The Molecules of Cell

WHY DO ISOMERS HAVE DIFFERENT PROPERTIES?
The chemical properties of compounds are decided by the way the compounds react in different environments which is in turn decided by the need for bonding. Isomers are compounds with same molecular formula but different structural formula. This means that though the number of carbon and hydrogen atoms are the same, the bonding is different, and so one might be an alkane while another of the isomer could be an alcohol all meaning they react in pretty different ways. For example, CH3CH2OH and CH3OCH3 are structural isomers but have different boiling points.

WHAT IS HFCS? WHY IS THERE A PROLEM WITH IT?

HFCS is made from corn, and in the mid 1970s we had an excess of corn crops in America. At the same time sugar prices were high, which meant that food prices were higher for the consumer. It was very cheap to produce and at the same time, it was six times sweeter than cane sugar. This is how it started. However there is a problem with HFCS. Sucrose and dextrose can both be broken down in your body before they ever make it to our liver, however fructose does not. It reaches to your liver. HFCS is used for fast food, sodas, cereal, energy bars, and more. Scientists found out that not fructose cause the body to burn sugar as opposed to burning fat. It has been found that our metabolism veers towards fat storage when consuming high levels of fructose. Therefore, HFCS contributes to obesity not only by our brains don't know that our stomachs are full, but also by causing the body to burn sugar rather than fat in our cells.

WHAT ARE THE BAD AFFECTIONS FOR USING ANABOLIC STEROIDS?
Anabolic steroids can harm your health by long-term use or excessive doses. These effects include harmful changes in cholesterol levels. It causes acne, high blood pressure, liver damage, and dangerous changes in the structure of the left ventricle of the heart. Also if you are a sport man, muscle that is built by steroids is considered as cheating. You are not allowed to use steroids. Steroids are only sold at a black market which smuggled or even counterfeit drugs are sold to users.


KEY TERMS
-Carbon Skeleton: the chain of carbon atoms in an organic molecule
-Isomer: compounds with the same formula but different structures
-Hydroxyl Group: consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to the carbon skeleton
-Carbonyl Group: linked by a double bond to an oxygen atom. If the carbon of the carbonyl group is at the end of a carbon skeleton, the compound is called an aldehyde. If it's within the chain, the compound is called a ketone
-Carboxyl Group: consists of a carbon double-bonded to an oxygen and also bonded to a hydroxyl group. It acts as an acid by contributing an H+ to a solution and becoming ionized
-Amino Group: composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton. It acts as a base by picking up an H+ from a solution.
-Phosphate Group: consists of a phosphorus atom bonded to four oxygen atoms. It's usually ionized and attached to the carbon skeleton by one of its oxygen atoms
-Methyl Group: consists of a carbon bonded to three hydrogens
-Enzymes: specialized macromolecules that speed up chemical reactions in cells
-Glycogen: excess sugar that animals store in the form of another glucose polysaccharide

-Phospholipids: the major component of cell membranes. They contain TWO fatty acids attached to glycerol

SUMMARY
     Most of the molecules that a cell makes are composed of carbon atoms. Those molecules, carbon-based, are called organic compounds. Carbon shares electrons with other atoms in four covalent bonds. Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons. Carbon skeleton, the chain of carbon in an organic molecule, can be unbranched as in butane, or branched, as in isobutane. It also includes double bonds, as in 1-butene and 2-butene. They have the same molecular formula, C4H8, but differ in the position of their double bond. Those compounds are called isomers. To determine the properties of organic compounds, we separate them into six chemical groups by their characteristics.
1) Hydroxyl group
2) Carbonyl group
3) Carboxyl group
4) Amino group
5) Phosphate group
6) Methyl group
     There are four main classes of large biological molecules. Carbohydrates, lipids, proteins, and nucleic acids. Cells make macromolecules by joining smaller molecules into chains called polymers. Polymers can be broken down. To digest them, a cell carries out hydrolysis, which is to add water and makes them into OH and H.
     Monosaccharides(CH2O) are the simplest carbohydrates. For example, glucose and fructose are two of them. These can form more complex sugars by hooking with single-unit sugars. Cells construct a disaccharide from two monosaccharides by dehydrating. By dehydration reaction, one oxygen will be left, which is called maltose. HFCS is cheaper than sugar and easier to mix into drinks and processed food since fructose is used, instead of glucose. However it has a problem for obesity. Animals store excess sugar in the form of another glucose polysaccharide, called glycogen in our liver and muscle cells.  Cellulose is the most abundant organic compound on Earth. It is a polymer of glucose. Most animals do not have enzymes that can hydrolyze the glucose linkages in cellulose, so it is not a nutrient for humans. However it contributes to digestive system health. Insects use chitin and crustaceans to build their exoskeleton.
     We store lipids in our body. A fat is a large lipid made from two kinds of smaller molecules, used for energy storage. Cells cannot exist without phospholipids, the major component of cell membranes. They are similar to fats but they contain two fatty acids, instead of three. Anabolic steroids are are synthetic variants of the male hormone testosterone. It builds up muscle and bone mass in males, but it is considered as drug, and it is illegal to use it for human body. Proteins are essential to the structures and functions of life. It is constructed from amino acid monomers. They structure cells, and organisms and participate in everything they do. Proteins need amino acids to like by peptide bonds. A protein has a specific shape that determines its function. The dependence of protein function on a protein's specific shape becomes clear when proteins are altered. In a process called denaturation, polypeptide chains unravel, losing their specific shape and, as a result, their function.
     The primary structure of a protein is its unique sequence of amino acids. In it, there is a secondary structure that holds alpha helix and pleated sheet. There is tertiary structure that has polypeptide, single subunit of transthyretin. And then quaternary structure, that has transthyretin, with four identical polypeptide subunits.

This diagram shows a dehydration reaction builds a polymer chain. The short polymer ends with H. And a monomer starts with HO, and ends with H. Between the short polymer and the monomer, H and HO form H2O, and the short polymer and the monomer get together to make a longer polymer. This is a dehydration reaction. It happens a lot our bodies. 


5 FACTS: 
1) Most of the world population is lack of lactase. We are not able to digest milk based food.
2) Organic compounds are the carbon based compounds.
3) Hydrophobic is water fear. It does not dissolve in water. Hydrophilic dissolves in water easily.
4) There are six functional groups. They are all hydrophilic, but methane. Also they are similar.
5) The four basic biological molecules. Carbohydrate, Protein, Lipid, Nucleic Acid.

Ch.2 The Chemical Basis of Life

WHAT HAPPENS IF WE ARE LACK OF TRACE ELEMENTS?
If you are lack of trace elements, it means that you are not getting enough nutrition for your body. You always need enough trace elements and minerals in your body. They have three important functions.
1) Structural components of body organs and tissues.
2) Constituents of body fluids and tissues as electrolytes concerned with body fluid balance, acid-base balance, membrane permeability, tissue irritability.
3) Catalysts in enzyme and hormone systems.
Those functions will stop working in your body. To prevent making those functions stop working, trace elements are needed in your body.

WHY DO WE USE RADIOACTIVE ISOTOPE IF IT COULD HARM US?
Since minute traces of radioactive isotopes can be sensitively detected by means of the Geiger counter and other methods, such as they use in medical therapy, diagnosis, and research. In therapy, they are used to kill or inhibit specific malfunctioning cells. There are many ways to use radioactive isotopes in our lives.


HOW CAN WATER STRIDERS WALK ON WATER? WHAT DOES IT HAVE TO DO WITH SURFACE TENSION?
Surface tension is a measure of how difficult it is to stretch or break the surface of liquid. Hydrogen bonds give water unusually high surface tension, making it behave as though it were coated with an invisible film. It is composed of thousands of molecules of water. They bond together, but it is also easy to break the bond. Therefore, when people try to walk on the water, we break the bonds and we sink in the water. However, water striders are too light to break the bonds. Therefore they are able to walk on the water without breaking them.


KEY TERMS
-Matter: anything that occupies space and has mass
-Element: a substance that cannot be broken down to other substances by ordinary chemical means
-Trace Elements: essential elements, but only in minute quantities
-Compound: a substance consisting of two or more different elements combined in a fixed ratio
-Isotopes: atoms that have the same numbers of protons and electrons and behave identically in chemical reactions, but they have different numbers of neutrons
-Ion: an atom or molecule with an electrical charge resulting from a gain or loss of one or more electrons
-Covalent Bond: when two atoms share one or more pairs of outer-shell electrons
-Polar Covalent Bond: the bonds of molecules that are sharing electrons unequally. In this bond, the pulling of shared, negatively charged electrons closer to the more electronegative atom makes that atom partially positive
-Cohesion: the tendency of hydrogen-bonded molecules stick together
-Adhesion: the clinging of one substance to another

SUMMARY
This chapter talks about chemistry the most because studying the structures and functions of living organisms is necessary to learn about life. Living organisms are all composed of matter, which is anything that occupies space and has mass. Matter is composed of elements which are substances that cannot be broken down to other substance by ordinary chemical means. All discovered elements are on periodic table. Trace elements are essential but only in minute quantities. For example, we need one of trace elements, iodine, for our bodies. If you do not take any, you will get goiter. Therefore people add iodine purposely to table salt to improve health. Chemicals are added to food to make it more nutritious, or simply make it look better. Elements also can combine to form compounds, such as H2O. H2(hydrogen) and O2(oxygen) combine and form H2O(water).
Atom is the smallest unit of matter. It consists of protons, electrons, and neutrons. protons and neutrons are tightly packed and electrons are around it. This packed protons and neutrons are called nucleus. The number of protons is called atomic number, and the sum of the protons and neutrons in nucleus is called mass number. Atomic mass is approximately equal to its mass number. Radioactive isotopes are useful as tracers in research on the chemistry of life because organisms incorporate radioactive isotopes of of an element into their molecules just as they do non-radioactive isotopes, and researchers can use special scanning devices to detect the presence of the radioactive isotopes, but it also can be harmful.
Electrons occur only at certain energy levels, called electron shells. For example, hydrogen only has 1 electron, so first shell holds it. However neon has 10 electrons so first shell cannot hold all of them. Thus it has second shell that holds the rest. When two ions with opposite charges attract each other, it is called ionic bond. Salt, NaCl, is an example. When two or more atoms share outer shell electrons, it is called covalent bond. For example, two hydrogen atoms share their electrons, it will turn H2, hydrogen. When hydrogen bonds some other elements, it is called hydrogen bond. It is a weak bond, but it is important in the chemistry of life. There are two types of conditions in the chemistry of life. Acidic and basic conditions. If the number is between 0 to 6 on pH scale, it is acid. If the number is between 8 to 14, it is base. If the number is 7, it is neutral, water.

Mass of ice is lighter than mass of liquid water as you can tell from the diagram. In liquid water, they do not have bonds, so it is easy to change shape. However they have stable bonds in ice, so it does not change shape easily. Also there are not many molecules in the ice so it is lighter than liquid water, which means it flows in the water.

5 FACTS:
1) Living things are all composed of matter.
2) We need 25 essential elements, trace elements, in our bodies always. Such as iron. They prevent disease.
3) An atom is composed of neutron, proton, and electron.
4) Chemical bonds occur depending on number of electrons on the outer shell.
5) Water has more dense than ice. This is because atoms in the ice do not move. They are stuck in the ice.

Ch.1 Exploring Life

WHAT DOES IT MEAN IF SOMETHING IS LIVING?
If something is living, that means that something interacts with its environments, exchanging matter and energy. Also living things are all made of cells. So I think that if something is living, means it has at least one cell or more in its body. Also living things reproduce, grow, develop, and change. Those are the things they all perform. All living things have a lot of performances in common. Also they are responsible to their own environments. What it means by exchanging matter and energy is that if a tree produces H2O from CO2, human breathes H2O which is produced by the tree. And the human exhales CO2 from H2O, the tree gets CO2. This is exchanging matter and energy.

WHY ARE CELLS THE BASIC UNITS OF LIFE?
Because cells are the smallest in the body. Also they are the lowest level in the hierarchy of biological organization at the properties of life emerge. All of our bodies are composed of cells and cells are made from other cells which shows that the cells are the lowest level. Scientists learn about growth, reproduction, and all other functions that living things perform by studying cells because they are all performed by cells. The cell theory holds true for all living things, no matter what. Because They are common to all living things, they can provide information about all life.

WHAT IS NATURAL SELECTION?
Natural selection is the process by which traits become more or less common in a population due to consistent effects upon the survival or reproduction of their bearers. It is a key word of evolution. The natural genetic variation within a population of organisms cause some individuals to survive and reproduce more successfully than others in their current environment. It basically is a process in organisms with certain inherited characteristics are more likely to survive and reproduce than are organisms with other characteristics.


10 Key Terms
-Biosphere: All the environments on Earth that support life.
-Ecosystem: All the organisms living in a particular area, and the nonliving physical components that living things need.
-Organelle: Membrane-bound structure that performs a specific function in a cell.
-Emergent Properties: The property where living things become more and more complex as it goes from cellular level.
-Producers: Photosynthetic organisms that provide the food for a typical ecosystem.
-Consumers: Organisms that eat plants and other animals to live.
-Genes: The units of inheritance that transmit information from parents to children.
-Prokaryotes: Archaea. Most live in Earth's extreme environments, such as salty lakes and hot springs.
-Science: To know. The way of knowing.
-Inductive Reasoning: Discovery science can lead to important conclusion based on a type of logic. For example "All organisms are made of cells."
-Deductive Reasoning: The logic used in hypothesis-based science to come up with ways to test hypotheses.


Explanation of Diagram

This is a diagram of eukaryotic cell.
It is subdivided by internal membranes into many different functional compartments or organelles, including the nucleus that houses the cell's DNA. It is bigger and more complicated than prokaryotic cell. Animals, plants, and fungi are composed of eukaryotic cells.








Summary of Chapter 1
All the living things are composed of at least one cell or more. There are two types of cells, one is a prokaryotic cell which compose only bacteria, and the other one is called eukaryotic cell which compose animals, plants, and fungi. All cells have DNA, and the continuity of life is based on this. DNA is a genetic material that has information from parents to offspring. They are similar to the way we arrange letter of the alphabet into precise sequences with specific meanings. Since there are tons of species, we decided to separate them into couple groups, such as three domains which are bacteria, eukarya, and archaea. In the domain, there are kingdoms. This is how we put all the organisms in several groups. In 1859, Charles Darwin published books about evolution. He talked about the idea of evolution. Also he pointed out that to propose a mechanism for evolution is called natural selection. Those books were immediate bestseller.
Scientists use two main approaches to learn about nature. One is called discovery science, and the other is called hypothesis-based science. Discovery science leads to important conclusions based on a type of logic called inductive reasoning. On hypothesis-based science, you make a hypothesis from your questions, and test it, then see what the result is. Those approaches could develop the technology because biology, technology, and society are connected. New discoveries of science can lead to new technologies. Also new technologies can lead to new scientific discoveries. If the technology improves, society improves as well. Evolution is connected to our everyday lives. Your cells develop depends on your environment. For instance, a giraffe's neck got so much longer than the past because it was easier for them to eat with long neck. They learned so that now their DNA makes their necks long like now.

5 FACTS:
1) All the living things perform seven things. Order, regulation, grow and develop, process energy, responsible for the environment, reproduce, evolutionary adaption.
2) Charles Darwin wrote a book about evolution and natural selection. The books became best seller.
3) Two types of discovery. Using hypothesis and leading to the result from many small facts.
4) Technology and science are related. Science leads to the new high technology things. Also Technology can lead to the new discovery of science.
5) Three types of domains. Bacteria(similar to archaea), Archaea(living in extreme environment), and Eukarya (having the most complex cell).