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X-ray crystallography was originally a means of determining the nature of X-rays, and was never supposed to be a research tool. X-ray crystallography is a process of determining the arrangement of atoms within crystals. In x-ray crystallography, x-rays strike a crystal and diffract into many specific directions, giving a crystallographer the means by which he can produce a three-dimensional picture of the density of electrons within the crystal. Max von Laue developed a law that connects the scattering angles and the size and orientation of the unit-cell spacings in the crystal, for which he was awarded the Nobel Prize in Physics in 1914 (Dana 28). This allows the positions of the atoms in the crystal to be determined, as well as their chemical bonds, their disorder and other information that is quite useful. Since many materials can form crystals, x-ray crystallography is crucial in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among various materials, especially minerals and alloys. The distribution of electrons in the table-salt structure showed that crystals are not necessarily composed of covalently bonded molecules, and proved the existence of ionic compounds (Bragg 43). The method also revealed the structure and functioning of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA. One of the most important applications of X-ray crystallography is its use in synthesizing substances. Before a chemist can synthesize a substance, a map of its atomic structure is drawn through X-ray crystallography. Dorothy Crowfoot Hodgkin made great advances in solving the structures of biological molecules including cholesterol, vitamin B12 and penicillin, for which she was awarded the Nobel Prize in Chemistry in 1964. In 1969, she succeeded in solving the structure of insulin after more than thirty years of research. X-ray crystallography is still the chief method for characterizing the atomic structure of new materials and in discerning materials that appear similar by other experiments. X-ray crystal structures can also account for unusual electronic or elastic properties of a material, shed light on chemical interactions and processes, or serve as the basis for designing pharmaceuticals against diseases. X-ray crystallography arose from the dynamical theory of diffraction, which describes the interaction of waves with a regular lattice. In this case, the waves are X-rays, and the regular lattice is a crystal. This has also led to many other diffraction techniques including neutron and electron diffraction, X-ray imaging, and other methods of crystallography such as electron crystallography. The development of X-ray crystallography also created the science of mineralogy. After determining the inner structures of many minerals, mineralogists were able to define the major mineral groups. The understanding that stems from crystallography has also allowed scientists to synthesize minerals used in industry. Consequently, it may even be possible to synthesize valuable minerals or even fossil fuels in the near future.
Dana, Edward. A Textbook of Mineralogy. 4th edition. New York: John Wiley & Sons, 1932.
Bragg, W. Lawrence. "XLIII. The Distribution of Electrons Around the Nucleus in the
Sodium and Chlorine Atoms" Philosophical Magazine Series 6 44.261 (1922). 17 Jul.
2010. < http://www.informaworld.com/10.1080/14786440908565188 >
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3-Properties of Water
Water is commonly known as the liquid of life. However, the reasons for why water makes up on average 70% of most organisms and covers 70% of the planets surface are very complex. Water's many unique physical and chemical properties that make life on Earth possible. Water is transparent, and consequently, aquatic plants can live within the water because sunlight can reach them. The structure of water makes much of this possible. Water molecules are bent downwards in a sort of shape. Since the water molecule is not linear and the oxygen atom has a higher electronegativity than hydrogen atoms, it carries a slight negative charge, whereas the hydrogen atoms are slightly positive. As a result, water is a polar molecule with. The net interactions between the dipoles on each molecule cause water's high surface tension. This dipolar nature contributes to water molecules' tendency to form hydrogen bonds which cause water's many special properties. The polar nature also favors adhesion to other materials. Because water is a dipolar molecule, water molecules' tend to form hydrogen bonds. A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as oxygen. The hydrogen must be covalently bonded to another electronegative atom to create the bond. Water has strong cohesion as each molecule may make four hydrogen bonds to other water molecules in a tetrahedral configuration. Water's polarity also causes its adhesion to many substances, and the cooperation of cohesion and adhesion overcomes gravity and reverse capillary action occurs. While capillary action usually results in an upward crescent of liquid in a thin tube, water moves downward against the flow of gravity. Since the molecules on the surface of the liquid are not surrounded by like molecules on all sides, they are attracted most to molecules on the surface, which, in turn, causes the surface portion of liquid to be attracted to another surface. The polarity of water is why it is considered the world's greatest solvent. Its polarity dissolves ionic bonds, which then forms a variety of solutions. Water also has a high specific heat. Hydrogen bonds provide a place where heat may be stored as potential energy of vibration, even at comparatively low temperatures. This accounts for water's high specific heat, far greater than any substance excluding pure hydrogen gas. This is the reason coastal areas generally have milder climates than inland regions, as water can store and withdraw heat. The high specific heat of water also tends to stabilize ocean temperatures, creating a favorable environment for marine life. Consequently, due to the high specific heat of water, temperature changes on land and in water remain within limits that permit life. Additionally, since organisms are primarily made of water, they are more capable of resisting internal temperature change than if they were made of a liquid with a lower specific heat. Because of all these remarkable properties, it can be ascertained that water is indeed the liquid of life.
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Many substances - for example, salt and sucrose - dissolve quickly in water
World's greatest solvent
Sweating and the evaporation of sweat from the body surface help reduce a human's body temperature
High specific heat
If you touch the edge of a paper towel to a drop of coloured water, the water will move up into (or be absorbed by) the towel.
During the winter, air temperatures in the northern U.S. can remain below 0°C for months; however, the fish and other animals living in the lakes survive.
High specific heat
Lungs and gills are moist to allow for efficient diffusion of gases
World's greatest solvent
Plasma and cytoplasm are water based.
World's greatest solvent
5- Elements and compounds of Nature
Distinguish between an element and a compound.
An element is made up of only one type of matter, divisible to a single atom with a unique number of protons, neutrons and electrons. A compound is made up of one or more elements. Elements are the simplest forms of matter that can exist under normal laboratory conditions. Elements cannot be separated into simpler substances by chemical means. They are the building blocks for all other substances. Oxygen, hydrogen, and carbon are examples of elements. Compounds are substances that can be separated into simpler substances only by chemical means. There are a variety of chemical processes that can be used to separate compounds into simpler substances. Salt is made up of the elements sodium and chloride. Water is made up of the elements hydrogen and oxygen. A compound is a substance formed when two or more elements are chemically joined. Water, salt, and sugar are examples of compounds. When the elements are joined, the atoms lose their individual properties and have different properties from the elements they are composed of. A chemical formula is used a quick way to show the composition of compounds. Letters, numbers, and symbols are used to represent elements and the number of elements in each compound.
Identify the 4 elements that make up 96% of living matter.
Carbon (C), Oxygen (O), Nitrogen (N) and Hydrogen (H)
Sketch an atom of carbon showing the location and number of electrons, protons, and neutrons. List the atomic number, atomic mass, and valence.
Atomic number: 14
Atomic mass: 12.011
Valence electrons: 4
List 3 examples of how radioactive isotopes can be useful to biologists.
Radioactivity tracers are used in the study of plants and animals.
Carbon-14 dating allows biologists to determine the age of various materials.
Phosphorus-32 is widely used for labeling nucleic acids and phosphoproteins
For each of the following elements, S, Ca, P, Fe, and Na, state a role in plants, animals, and prokaryotes. The role can be same for all three groups.
S- Sulfur is an essential component of all living cells.
Sulfur is absorbed by plants from soil through its roots.
Sulfur may also serve as chemical food source for primitive organisms.
Ca- Ca2+ ions are an essential component of plant cell walls and membranes
Calcium in mammals is necessary for many enzymes, as well as in maintaining bone structure and as a cell regulator
Calcium in bacteria is a common signalling method
P- Phosphorus is a key element in all known forms of life.
Phosphorus is an essential mineral for plant growth
Phosphorus in animals is primarily in the form of ATP
Phosphorus is a major component is the phospholipid bilayer of cell membranes
Fe- Iron is a necessary trace element found in nearly all living organisms
Iron is an important mineral for plant growth
Iron is a major component in hemoglobin in animals
Iron also plays a role in prokaryotic metabolism
What influences the chemical behaviour (bonding capabilities) of an atom?
Electron configuration is the biggest influence on chemical behavior. The most important consideration is valence electrons. All atoms want a full outer shell as with the noble gases. To achieve this, they will react in order to lose, gain, or share electrons. When metals and non-metals react together, you often get complete transfer of electrons from the metal to the non-metal. The ions formed are held together by the attraction of the opposing charges. This is ionic bonding. When chemical reactions occur, they are generally merely rearranging the atoms to make the electron configurations as close as possible to the stable noble gases.
Distinguish among non-polar covalent, polar covalent, and ionic bonds.
A non-polar covalent bond is a bond in which electrons are shared equally between atoms
A polar covalent bond is a covalent bond with an imbalance of charge
An ionic bond is similar to a polar covalent but with a greater charge imbalance; a metal cation and a nonmetal anion bond to become neutral
Describe how a molecule's shape influences its biological function, using a specific enzyme-substrate complex as an example.
A molecule's shape may affect its function in many different ways ways. For example, VSEPR theory allows scientists to predict the shape of covalent compounds and each shape results in various properties. Diamond is also very sturdy because of its structure. One of the most drastic example of shape affecting function is in enzymes. Because of the enzyme's shape, each enzyme may only be catalyzed by a very specific substrate. As a result, biologists may very selectively observe various catalysis reactions based on which substrate is present.
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6-pH of nature
Write the equation for the dissociation and re-formation of water
What does pH measure? Describe the pH scale.
pH is a measure of the acidity or basicity of a solution on a scale of 14. 7 is pure water which is neutral, and an acid or a base is lower or higher than 7 respectively. The pH scale is logarithmic and as a result, each whole pH value below 7 is ten times more acidic than the next higher value. For example, pH 4 is ten times more acidic than pH 5 and 100 times (10 times 10) more acidic than pH 6. The same holds true for pH values above 7, each of which is ten times more alkaline (another way to say basic) than the next lower whole value. For example, pH 10 is ten times more alkaline than pH 9 and 100 times (10 times 10) more alkaline than pH 8.
Using the bicarbonate buffer system as an example, explain how buffers work.
A buffer solution is an aqueous solution consisting of a mixture of a weak acid and its conjugate base vice versa. Buffer solutions are used as a means of keeping pH at a nearly constant value in a wide variety of chemical applications. Many life forms thrive only in a relatively small pH range; an example of a buffer solution is blood.
Describe the causes of acid precipitation and how it affects the environment.
Acid rain is a rain that is unusually acidic It is very harmful to plants, aquatic animals, and infrastructure through the process of wet deposition. Acid rain is often caused by industrial emissions of compounds containing ammonium, carbon, nitrogen, and sulfur, which react with the water molecules in the atmosphere to produce acids. However, the splitting of nitrogen compounds by lightning or the release of sulfur dioxide into the atmosphere by volcanic eruption also causes it naturally.
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7- Organic chemistry
As far as biological molecules are concerned, appearance does very much affect function. Each biological important molecule (carbohydrates, lipids, proteins, nucleic acids) has a different shape or structure, and thus a separate function. Carbohydrates contain carbon and water, both of which are necessary for life and are consequently very important in the human body. Its structure consists of chains of carbon, with hydrogen and hydroxide molecules alternating on either side, which allows for increased bonding on either side. Carbohydrates are part of energy reactions involving ATP, a fundamental component in recognition sites on cell surfaces, and one of three essential components of DNA and RNA. Carbohydrates are also an important part of redox reactions that occur in nature. They are also useful in providing energy and regulation of blood glucose and in the breakdown of lipids. The lipids are a large and diverse group of naturally occurring organic compounds. Lipids also have a carbon-based structure. Phospholipids are the main constituents of cell membranes which are hydrophobic and help to regulate movement in and out of the cells i.e. phospholipids molecules can move about in their half the bilayer, but there is a significant energy barrier preventing migration to the other side of the bilayer. Lipids also have a higher calorific value than carbohydrates as energy storage. This is due to the fact that although they are both hydrocarbons, lipids contain very little water, which allows for more efficient energy storage. Proteins on the other hand are not carbon based, but rather are long chains of various connected amino acids, and are thus very versatile. Proteins hold together, protect, and provide structure to the human body In the form of enzymes, hormones, antibodies, and globulins, they catalyze, regulate, and protect the body chemistry. This versatility make protein very important in the human body. Proteins are differentiated by the amino acids that make up each respective protein. The twenty amino acids are the primary components of proteins, their incorporation regulated by the genetic code. Many other naturally occurring amino acids exist, and must thus be consumed in food. The primary structure refers to the sequence of the different amino acids of the peptide or protein. The primary structure is held together by covalent or peptide bonds, which are made during the process of protein biosynthesis or translation. Nucleic acids are the most important molecule biologically. Nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are the genetic material of cells. Nucleic acids bond in spiraling "ladders" of nucleotides, which is quite useful in its function. Each DNA strand holds the same genetic information, so both strands can serve as templates for the reproduction of the opposite strand. Hence, the resulting double-stranded DNA molecules are identical. To access this information the pattern must be "read" in a linear fashion, just as a bar code is read at a supermarket checkout. Because living organisms are extremely complex, a correspondingly large amount of information related to this complexity must be stored in the DNA. Each biological molecule has a different shape and size, and thus a different function. These various function thus makes the human body very complex.
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8- Section 1-Glucose
Sketch glucose and ribose.
Glucose â†‘ Riboseâ†‘
Sketch sucrose, highlighting a glycosidic linkage
List 4 examples of other saccharides and state the function of each.
How are starch and cellulose structurally different and how does this difference impact on biological systems?
You can eat starch, but you cannot digest cellulose. Your body contains enzymes that break starch down into glucose to fuel your body. Humans do not have enzymes that can break down cellulose. Some animals do, like termites, who eat wood, or cattle, who eat grass, and break down cellulose in their four-chambered stomachs. Cellulose is much stronger than starch. Starch is practically useless as a material, but cellulose is strong enough to make fibers from, and hence rope, clothing, etc. Cellulose does not dissolve in water the way starch will, and does not break down as easily. Dissolving in water would be a little inconvenient in clothes. Furthermore, rain would wash away all wooden houses, park benches, and playground equipment if cellulose were soluble in water.
Fructose- Fructose is ,like glucose, a quick source of energy. But it also has a different structure, and has a different effect on plant cells
Galactose- Galactose is a nutritive sweetener present with glucose as lactose in milk. It's also a component of the antigens present on blood cells that determine blood type
Xylose- Xylose is the main building block for hemicellulose, which makes up 30% of plant matter.
Cellulose- Cellulose makes up much of the structure of plant cell walls. It is present in wood and cotton in large quantities.
Section 2: Polysaccharide
etches of a starch and cellulose. Make sure that the sketch clearly shows the difference of both.
Plants store glucose as starch. The structure of starch consists of long polymer chains of glucose units connected by an alpha acetal linkage. Because the links are regular, it can be easily broken down
Cellulose is a rigid polysaccharide that makes up much of plants. The acetal linkage is beta which makes it different from starch. This peculiar difference in acetal linkages results in a lack of digestibility in humans.
Section 3: Lipids and Esters
Saturated fat is fat that consists of triglycerides containing only saturated fatty acid radicals. There are several kinds of naturally occurring saturated fatty acids, which differ by the number of carbon atoms. Saturated fatty acids have no double bonds between the carbon atoms of the fatty acid chain and are thus fully saturated with hydrogen atoms.
Unsaturated fat has a single double bond in the fatty acid chain and all of the remainder of the carbon atoms in the chain are single-bonded. Fatty acid viscosity (thickness) and melting temperature increases with decreasing number of double bonds. Therefore, monounsaturated fatty acids have a lower melting point than saturated fatty acids. Consequently, they are less likely to remain solid in arteries and are thus healthier.
The C-H bond is a weak bond, which means that it stores a lot of energy. Carbohydrates are useful for short-term energy storage because they can be used for cellular respiration most efficiently. Lipids, however, are used for long-term energy storage because they have many C-H bonds. The drawback to lipids is that they must undergo oxidation and other reactions before undergoing cellular respiration. Consequently, they are both used to store energy because they are both hydrocarbons.
Section 4: Protein
Type of Protein
Major component of muscle
Maintains toughness of skin and nails
Transport oxygen in blood
Section 5: DNA structure
Purine is a nitrogenous base which has two carbon-nitrogen rings (adenine and guanine) while pyramidine only has one carbon-nitrogen ring (thymine and cytosine).
DNA contains the information that creates proteins
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9- AP Essay
Proteins play central roles both as building blocks of the human body. The 20 amino acids that are found within proteins convey a vast array of chemical versatility. The precise amino acid content, and the sequence of those amino acids, of a specific protein, is determined by the sequence of the bases in the gene that encodes that protein. The chemical properties of the amino acids of proteins determine the biological activity of the protein. Proteins not only catalyze all (or most) of the reactions in living cells, they control virtually all cellular process. In addition, proteins contain within their amino acid sequences the necessary information to determine how that protein will fold into a three dimensional structure, and the stability of the resulting structure. The three types of bonds found within proteins are as follows: hydrogen bonds, ionic bonds, disulfide bonds. Each type of bond plays a specific role in the protein's behavior. In the secondary structure of proteins, hydrogen bonds form between the backbone oxygens and amide hydrogens. This in turn determines the proteins role. Ionic bonds on the other hand, hold the protein together, like cement. Disulfide bonds are responsible for stabilizing the protein and its respective ingredients. Protein structure is crucial to regulation of enzyme activity. Proteins work by fitting in with different proteins and biological molecules through enzyme reaction. Essentially, the structure of a protein is enzyme-centric. Proteins often bind with enzymes to control their activity. This can increase or decrease enzymatic activity depending on how the protein is affecting the enzyme's active site, binding site, and other factors. Hemoglobin, a blood protein, is crucial in carrying oxygen. Abnormal hemoglobin is often a sign of sickle cell anemia. Sickling decreases the cells' flexibility and results in a risk of various complications. The sickling occurs because of a mutation in the hemoglobin gene. Life expectancy is shortened, with studies reporting an average life expectancy of 42 in males and 48 in females. Sickle-cell anemia, usually occurs more commonly in people (or their descendants) from parts of tropical and sub-tropical regions where malaria is or was common. One-third of all indigenous inhabitants of Sub-Saharan Africa carry the gene, because in areas where malaria is common, there is a survival value in carrying only a single sickle-cell gene. Those with only one of the two alleles of the sickle-cell disease are more resistant to malaria, since the infestation of the malaria plasmodium in to blood cells is halted by the sickling of said cells. Those infected with malaria without sickle cell anemia halting the disease usually die, leading to an increase in the proportion of people with sickle cell disease. Consequently, sickle cell disease is considered selected for in sub-Saharan Africa.
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13- Heterotroph hypothesis
The heterotrophic hypothesis, also known as the Haldane-Oparin hypothesis after two scientists who independently proposed it, argues that life in the form of organic molecules could have formed from inorganic molecules. Much research has been conducted to explain how life could spontaneously form. The general theme is that components of earth's atmosphere could form into complex organic molecules, which eventually would become life. One famous experiment by Stanley Miller and Harold Urey used water vapor, methane, hydrogen, and ammonia (along with an electrical spark) to show that organic molecules (e.g. amino acids) could form spontaneously. However, scientists no longer think the Earth's atmosphere resembled the Miller-Urey composition. Subsequent experiments have shown a rich variety of organic compounds can form from inorganic carbon sources in various types of atmospheres. The exact composition of Earth's atmosphere remains a subject of research, but the concept that complex molecules can spontaneously form seems well supported.