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Wednesday, September 1, 2010

DNA

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Assignments

BIOLOGY
Read: Chapter 5 ending on pg. 84.
Be sure to also look over the chapter review.


Assignment: (for Hallie, Tyler, Jeremy, Bobby, Fiona and Scott Michael)
Research 2 compounds and answer the following questions:
1. What elements combine to form the compounds and how do they chemically combine - polar or non-polar covalent bonds?
2. What are the characteristics of the individual elements and how does this differ from the emergent properties of the new compound?
3. Where are these compounds found and what method is used to retrieve them?
4. What uses do these compounds have?
5. Would there be a significant difference in our lives if either one of these compounds was not available to us?
Put this information together in a paper with diagrams, charts, maps or pictures.
This will be graded on content, depth of understanding, thoroughness, clarity of illustrations and other visual materials. Spelling, punctuation, grammar and mechanics are also an important part of your grade. First draft due Friday, 11/12 - pass in to Barbara.

Assignment: (for Cailee, Mackenzie, Will, and Connor)
Answer the following questions and put your answer together in the form of a Power Point presentation. You will be grades on content, understanding, thoroughness and clarity.
1. What is the difference between covalent and ionic bonding?
Give at least two examples of both?
2. From the examples given, what is the atomic number and mass of each of the elements involved? What is the difference between atomic mass and number?
3. Which groupings from the Periodic Table are the elements from (i.e. reactive metals, halogens, etc...). What is the valence structure like that allowed the covalent bonding to occur?
4.What are emergent properties and give a few examples of these properties from the compounds from question 1.
Due: Tuesday 11/16



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Biology Notes

Macromolecules Chapter 5

Cells join small organic molecules together to form larger molecules. The four main classes of large biological molecules are carbohydrates, lipids, proteins and nucleic acids. Many of these cellular molecules are, on the molecular scale, huge. Some proteins can consist of thousands of covalently bonded atoms that form a molecule weighing over 100,000 daltons. Biologists use the term macromolecule for such large molecules. The architecture of a macromolecule helps explain how that molecule works.

Polymers - A long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a train consists of a chain of cars. The large molecules in three of the four classes of life’s organic compounds: carbohydrates, proteins and nucleic acids, are polymers. The repeating units that serve as the building blocks of a polymer are small molecules called monomers. Some of the monomers also have other functions of their own.

Monomers are connected by a reaction in which two molecules are covalently bonded to each other through loss of a water molecule; this is called condensation reaction, specifically a dehydration reaction, because the molecule lost is water. When a bond forms between two monomers, each monomer contributes part of the water molecule that is lost: One molecule provides a hydroxyl group

(-OH), while the other provides a hydrogen (-H). To make a polymer, this reaction is repeated as monomers are added to the chain one by one. The cell must expend energy to carry out these dehydration reactions, and the process occurs only with the help of enzymes, specialized proteins that speed up chemical reactions in cells (figure 5.2- page 63).

Polymers are disassembled to monomers by hydrolysis, a process that is essentially the reverse of the dehydration reaction. Hydrolysis means to break with water. Bonds between molecules are broken by the addition of water molecules; a hydrogen from the water attaching to one monomer and a hydroxyl attaching to the adjacent monomer. (Remember the section about the polarity of water and how that makes compounds dissolve - page 46.) Digestion is an example of hydrolysis working in our bodies. The bulk of the organic material in our food is in the form of polymers that are much too large to enter our cells. Within the digestive tract, various enzymes attack the polymers, speeding up hydrolysis. The released monomers are then absorbed into the bloodstream for distribution to all body cells. Those cells can then use dehydration reactions to assemble the monomers into new polymers that differ from the ones that were digested.

The diversity of macromolecules in the living world is vast, and the potential variety is nearly limitless. Each cell in a living organism has thousands of different kinds of macromolecules; the collection varies from one type of cell to another in the same organism. The inherent differences between human siblings reflect variations in polymers, particularly DNA and proteins. Molecular differences between unrelated individuals are more extensive - and between species greater still.

Polymers are constructed from only 40 to 50 common monomers; however, the amount of combinations is huge, much like creating hundreds of thousands of words from only 26 letters of the alphabet. The key is arrangement - variations in the linear sequence the units follow. For example, proteins are built

from 20 kinds of amino acids arranged in chains that are typically hundreds of amino acids long.

Carbohydrates - Include both sugars and their polymers. The simplest carbohydrates are the monosaccharides, or single sugars, also known as simple sugars. Disaccharides are double sugars, consisting of two monosaccharides joined by condensation. The carbohydrates that are macromolecules are polysaccharides, polymers of many sugars. Most names for sugars end in ose.

Monosaccharides generally have molecular formulas that are some multiple of CH2O. Glucose (C6H12O6), the most common monosaccharide, is of central importance in the chemistry of life. Glucose and other monosaccharides are major nutrients for cells. In the process known as cellular respiration, cells extract the energy stored in glucose molecules. Not only are simple sugar molecules a major fuel for cellular work, but their carbon skeletons serve as raw material for the synthesis of other types of small organic molecules, such as amino acids and fatty acids. Sugar molecules that are not immediately used in these ways are generally incorporated as monomers into disaccharides or polysaccharides.

Disaccharides consist of two monosaccharides joined by a glycosidic linkage, a covalent bond formed between two monosaccharides by a dehydration reaction. Maltose is a disaccharide formed by the linking of two molecules of glucose. Maltose is an ingredient for brewing beer, malt sugar. The most prevalent disaccharide is sucrose, table sugar. Its two monomers are glucose and fructose. Plants generally transport carbohydrates from leaves to roots and other nonphotosynthetic organs in the form of sucrose. Lactose, the sugar present in milk, is another disaccharide, consisting of a glucose molecule joined to a galactose molecule.

Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells. Other polysaccharides serve as building material for structures that protect the cell or the whole organism.

Starch, a storage polysaccharide of plants, is a polymer consisting entirely of glucose monomers. Plants store starch as granules within cellular structures called plastids; including chloroplasts (figure 5.6a - page 66). By synthesizing starch, the plant can stockpile surplus glucose. Because glucose is a major cellular fuel, starch represents stored energy. The sugar can later be withdrawn from this carbohydrate bank by hydrolysis, which breaks the bonds between the glucose monomers. Most animals, including humans, also have enzymes that can hydrolyze plant starch, making glucose available as a nutrient for cells. Potatoes and grains, wheat, corn, rice and other grasses are the major sources of starch in the human diet.

Animals store a polysaccharide called glycogen, a polymer of glucose. Humans and other vertebrates store glycogen mainly in liver and muscle cells. Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases. This stored fuel cannot sustain an animal for long, however. In humans, for example, the glycogen bank is depleted in about a day unless it is replenished by consumption of food.

Organisms build strong materials from structural polysaccharides. For example, the polysaccharide called cellulose is a major component of the tough walls that enclose plant cells. On a global scale, plants produce almost 100 billion tons of cellulose per year; it is the most abundant organic compound on Earth. A cellulose molecule is straight, never branched. In plant cell walls, parallel cellulose molecules held together in this way are grouped into units called microfibrils. These cables are a strong building material for plants, as well as for humans who use wood, which is rich in cellulose.

Humans do not have enzymes to digest cellulose, in fact few organisms do. The cellulose fibrils in our food pass through the digestive tract and are eliminated with the feces. Along the way, however, the fibrils abrade the wall of the digestive tract and stimulate the lining to secrete mucus, which aids in the smooth passage of food through the tract. Thus, although cellulose is not a nutrient for humans, it is an important part of a healthy diet.

Chitin is another important structural polysaccharide. This is the carbohydrate used by arthropods (insects, spiders, crustaceans and related animals) to build their exoskeletons. An exoskeleton is a hard case that surrounds the soft parts of an animal. Pure chitin is leathery, but it becomes hardened when encrusted with calcium carbonate, a salt. Chitin is also found in many fungi, which use this polysaccharide rather than cellulose as the building material for their cell walls.

Lipids are the one class of large biological molecules that does not include polymers. The compounds called lipids are grouped together because they share one important trait: They have little or no affinity for water. Lipids consist of mostly hydrocarbons which gives it the hydrophobic behavior. Lipids include waxes, certain pigments, phospholipids, fats and steroids.

Although fats are not polymers, they are large molecules, and they are assembled from smaller molecules by dehydration reactions. A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids. A fatty acid has a long carbon skeleton, usually 16 to 18 carbon atoms in length. At one end of the fatty acid is a carboxyl group, the functional group that gives these molecules the name fatty acids (remember carboxyl molecules are acids). Attached to the carboxyl group is a long hydrocarbon chain. The nonpolar C-H bonds in the hydrocarbon chains of fatty acids are the reason fats are hydrophobic. In making a fat, three fatty acids each join to a glycerol molecule called the head. The resulting head with 3 tails is called a triacylglycerol, also called triglyceride, a word often found in the list of ingredients on packaged foods (page 69).

If there are no double bonds between the carbon atoms composing the chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton. Such a structure is described as being saturated with hydrogen, so the resulting fatty acid is called a saturated fatty acid. At room temperature, the molecules of a saturated fat are packed closely together, forming a solid like animal fats, lard and butter.

Unsaturated fatty acids have one or more double bonds, formed by the removal of hydrogen atoms from the carbon skeleton. Fats from plants and fish are generally unsaturated and are liquids at room temperature, for instance corn oil and cod liver oil. The kinks where the double bonds are located prevent the molecules from packing together closely enough to solidify at room temp. Hydrogenated vegetable oil means that unsaturated fats have been synthetically converted to saturated fats by adding hydrogen. Peanut butter and margarine are hydrogenated to prevent lipids from separating out in liquid (oil) form. Diets rich in saturated fats can contribute to cardiovascular disease. Deposits called plaques develop on the internal lining of blood vessels, impeding blood flow and reducing the resilience of the vessels.

The major function of fat is energy storage. The hydrocarbon chains of fats are similar to gasoline molecules and are just as rich in energy. Humans and other mammals stock their long-term food reserves in adipose cells which swell and shrink as fat is deposited and withdrawn from storage. In addition to storing energy, adipose tissue also cushions such vital organs as the kidneys, and a layer of fat beneath the skin insulates the body. This subcutaneous layer is especially thick in whales, seals and most other marine mammals.

Phospholipids, similar to fats but with only two fatty acid tails rather than three, form bilayers which are hydrophobic in the interior and this forms a boundary between the cell and its external environment. Phospholipids are major components of cell membranes (see diagram page 71).

Steroids are lipids characterized by a carbon skeleton consisting of four fused rings. Different steroids vary in the functional groups attached to this ensemble of rings (see diagram page 71). One steroid is cholesterol, a common component of animal cell membranes and is also the precursor from which other steroids are synthesized. Many hormones are steroids produced from cholesterol including the sex hormones.

Proteins account for more than 50% of the dry weight of most cells, and they are instrumental in almost everything organisms do. Proteins are used for structural support, storage, transport of other substances, signaling from one part of the organism to another, movement and defense against foreign substances. Some proteins regulate metabolism by selectively accelerating chemical reactions in the cell. These types of proteins are called enzymes. (Examples of the types of proteins is given in the chart of page 72)

Humans have tens of thousands of different proteins, each with a specific structure and function. Proteins are the most structurally sophisticated molecules known. They vary extensively in structure which leads to diverse functions. Proteins are all polymers constructed from the same set of 20 amino acids (chart page 72 & 73 lists all 20 amino acids). Polymers of amino acids are called polypeptides. A protein consists of one or more polypeptides folded and coiled into specific conformation.

Amino acids are organic molecules possessing both carboxyl and amino groups (see diagram on bottom of page 71). At the center of the amino acid is an asymmetric carbon atom called the alpha (α) carbon. Its four different partners are an amino group, a carboxyl group, a hydrogen atom and a variable group (symbolized by the letter R). The physical and chemical properties of the R group, also called the side chain, determine the unique characteristics of a particular amino acid.

When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, an enzyme can cause them to join by catalyzing a dehydration reaction. The new bond formed between amino acids is called a peptide bond. Repeated over and over, this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds. This new polypeptide has a backbone of the amino acids with all the various variable groups attached along the chain.

Each specific polypeptide has a unique linear sequence of amino acids which can range in length from a few monomers to a thousand or more. The immense variety of polypeptides in nature illustrates an important concept introduced earlier - that cells can make many different polymers by linking a limited set of monomers into diverse sequences. (This concept is much like taking the letters of the alphabet and arranging them into different words.)

A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape. It is the amino acid sequence of a polypeptide that determines what three-dimensional conformation the protein will take, some are globular and some are fibrous. A protein’s specific conformation determines how it works.

When a cell synthesizes a polypeptide, the chain generally folds spontaneously to assume the functional conformation for that protein. This folding is driven and reinforced by the formation of a variety of bonds between parts of the chain. Thus, the function of a protein - the ability of a receptor protein to identify and associate with a particular chemical messenger, for instance - is an emergent property resulting from exquisite molecular order.

There are 4 levels of structure to a protein: primary, secondary, tertiary and if the protein is made up of two or more polypeptide chains, quaternary.

Primary structure - is the unique sequence of amino acids (see diagram page 75).

Secondary structure - Most proteins have segments of their polypeptide chain repeatedly coiled or folded in patterns that contribute to the protein’s overall conformation. These coils and folds, collectively referred to as secondary structure, are the result of hydrogen bonds at regular intervals along the polypeptide backbone. Only the atoms of the backbone are involved, not the amino acid side chains. One such formation is the α helix, a delicate coil held together by hydrogen bonding. The other main type of secondary structure is the β pleated sheet, in which two or more regions of the polypeptide chain lie parallel to each other (see diagram page 76).

Tertiary structure - is irregular contortions from interactions between side chains of the various amino acids. Hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains, as well as van der Waals interactions, help stabilize tertiary structure. These are all weak interactions, but their cumulative effect helps give the protein a specific shape. The conformation of a protein may be reinforced further by strong, covalent bonds called disulfide bridges. As the interactions of the side chains cause folding to occur, some amino acids with sulfhydryl groups (-SH) on their side chains are brought together. The sulfur of one cysteine bonds to the sulfur of the second, and the disulfide bridge (-S-S-) rivets parts of the protein together (see diagram page 77).

Quaternary structure - is the overall protein structure that results from the aggregation of two or more polypeptide chains that have formed one functional macromolecule.

The amino acid sequence of a polypeptide is programmed by a unit of inheritance known as a gene. Genes consist of DNA, which is a polymer belonging to the class of compounds known as nucleic acids. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). These are the molecules that enable living organisms to reproduce their complex components from one generation to the next. DNA provides directions for its own replication. DNA also directs RNA synthesis and, through RNA, controls protein synthesis.

DNA is the genetic material that organisms inherit from their parents.

When a cell reproduces itself by dividing, its DNA molecules are copied and passed along from one generation of cells to the next. Encoded in the structure of DNA is the information that programs all the cell’s activities. DNA is like a computer program. It is encoded information that directs function, however, by itself, DNA does not get work done, it needs equipment to perform tasks. The tools for most biological functions consist of proteins. (Hemoglobin is the protein that carries oxygen in the blood.)

Each gene along the length of a DNA molecule directs the synthesis of a type of RNA called messenger RNA (mRNA). The mRNA interacts with the cell’s protein-synthesizing machinery to direct the production of a polypeptide. The actual sites of protein synthesis are cellular structures called ribosomes. In a eukaryotic cell, ribosomes are located in the cytoplasm, while the DNA is located in the nucleus. Messenger RNA relays instructions from the nucleus through the cytoplasm to the ribosomes. Prokaryotic cells lack a nucleus but still utilize mRNA to convey information from the DNA to the ribosomes and other cell equipment that translates the information to form amino acid sequences.

Nucleic acids are polymers of monomers called nucleotides. Each nucleotide is itself composed of three parts: an organic molecule called a nitrogenous base, a pentose (five-carbon sugar), and a phosphate group. There are 2 families of nitrogenous bases: pyrimidines and purines.

The members of the pyrimidines family are cytosine (C), thymine (T), and uracil (U).

The pyrimidines have a six-member ring of carbon and nitrogen atoms (see page 83).

The members of the purines are adenine (A) and guanine (G).

The purines are larger than the pyrimidines, with a six-membered ring fused to a five-membered ring.

Cytosine, adenine, and guanine are found in both RNA and DNA. Thymine is only found in DNA and uracil is only found in RNA.

The pentose (sugar molecule) connected to the nitrogenous base is ribose in the nucleotides of RNA and deoxyribose in DNA. A phosphate group attaches to the number 5 carbon of the pentose. The molecule is now a nucleoside monophosphate - a nucleotide.

In a nucleic acid polymer, or polynucleotide, nucleotides are joined by covalent bonds between the phosphate of one nucleotide and the sugar of the next. This bonding results in a backbone with repeating pattern of sugar-phosphate units. All along this sugar-phosphate backbone are appendages consisting of the nitrogenous bases (see page 83).

The sequence of bases along a DNA (or mRNA) polymer is unique for each gene (discrete unit of hereditary information). Because genes are hundreds to thousands of nucleotides long, the number of possible base sequences is effectively limitless. A gene’s meaning to the cell is encoded in its specific sequence of the four DNA bases (example: AGGTAACTT… has one meaning where GATAACGGTTA… has another). The linear order of bases in a gene specifies the amino acid sequence - the primary structure - of a protein, which in turn specifies that protein’s three-dimensional conformation and function in the cell.

RNA molecules of cells consist of a single polynucleotide chain (see page 83).

DNA molecules have two polynucleotides that spiral around an imaginary axis to form a double helix (see page 84). The two sugar-phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired in the interior of the helix. The two polynucleotides, or strands, are held together by hydrogen bonds between the paired bases and by van der Waals interactions between the stacked bases. Most DNA molecules are very long, with thousands or even millions of base pairs connecting the two chains. One long DNA double helix includes many genes, each one a particular segment of the molecule.

Only certain bases in the double helix are compatible with each other. Adenine (A) always pairs with thymine (T), and guanine (G) always pairs with cytosine (C). If we know the sequence along one strand we would also know the corresponding sequence of the other strand.

A ------ T

G ------- C

G ------- C

T ------- A

C ------- G

C ------- G

G ------- C

T ------- A

A ------- T

G ------- C

It is this feature of DNA that makes possible the precise copying of genes that is responsible for inheritance, that the sequence of bases always follows a precise order. In preparation for cell division, each of the two strands of a DNA molecule serves as a template to order nucleotides into a new complementary strand. The result is two identical copies of the original double-stranded DNA molecule, which are then distributed to the two daughter cells. Thus, the structure of DNA accounts for its function in transmitting genetic information whenever a cell reproduces.

Genes (DNA) and their products (proteins) document the hereditary background of an organism. The linear sequences of nucleotides in DNA molecules are passed from parents to offspring, and these DNA sequences determine the amino acid sequences of proteins. Siblings have greater similarity in their DNA and proteins than do unrelated individuals of the same species. If the evolutionary view of life is valid, we should be able to extend this concept of “molecular genealogy” to relationships between species: We should expect two species that appear to be closely related based on fossil and anatomical evident to also share a greater proportion of their DNA and protein sequences than do more distantly related species (see table 5.2 page 84).

Biology Notes

The Importance of Carbon Chapter 4

Of all chemical elements, carbon is unparalleled in its ability to form molecules that are large, complex and diverse. This molecular diversity has made possible the diversity of organisms that have evolved on Earth. Although a cell is composed of 70-95% water, the rest consists mostly of carbon-based compounds. Protein, DNA, carbohydrates, and other molecules that distinguish living matter from inanimate material are all composed of carbon atoms bonded to one another and to atoms of other elements. Water is the universal medium for life. Carbon is the universal building block of life. The most common elements found in living organisms are hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), phosphorus (P) and Carbon (C). Carbon accounts for the large diversity of biological molecules.

Organic Chemistry - The branch of chemistry that specializes in the study of carbon compounds. Compounds that contain carbon are said to be organic. Organic molecules range from simple molecules like carbon dioxide (CO2) and methane (CH4) to huge molecules such as proteins, with thousands of atoms. Most organic compounds contain hydrogen atoms as well.

Carbon has a total of 6 electrons: 2 in the first shell and 4 in the second (valence shell). Having 4 valence electrons in a shell that holds 8, carbon has little tendency to gain or lose electrons and form ionic bonds. Instead, carbon atoms usually complete their valence shell by sharing electrons with other atoms in four covalent bonds. Each carbon atom thus acts as an intersection point from which a molecule can branch off in up to four directions. This tetravalence is one facet of carbon’s versatility that makes large, complex molecules possible.

When carbon atoms form single covalent bonds , the arrangement of its four hybrid orbitals causes the bonds to angle toward the corners of an imaginary tetrahedron (see figure 2.17c - page 37). The bond angles in methane (CH4) are 109o and they are approximately the same in any group of atoms where carbon has four single bonds (see figure 4.2b - page 54). In molecules with still more carbons, every grouping of a carbon bonded to four other atoms has a tetrahedral shape. When two carbon atoms are joined by a double covalent bond, all bonds around those carbons are in the same plane (see figure 4.2c - page 54).

It is important to remember that molecules are three-dimensional and that the shape of a molecule often determines its function. The covalent bonding of carbon with oxygen, hydrogen, and nitrogen and the completion of the valence shells define the rules of covalent bonding in organic chemistry - the building code that governs the architecture of organic molecules.

CO2 - Carbon dioxide - Carbon shares its valence electrons with 2 oxygen atoms to complete the valence shells for all the atoms. The bonds are double covalent. Not necessarily considered to be organic, carbon dioxide is taken from the air by plants and incorporated into sugars and other foods during photosynthesis; CO2 is the source of carbon for all the organic molecules found in organisms.

Carbon chains form the skeletons of most organic molecules. The skeletons vary in length and may be straight, branched or arranged in closed rings (see figure 4.4 - page 55). Some carbon skeletons have double bonds, which vary in number and location. Such variation in carbon skeletons is one important

source of the molecular complexity and diversity that characterize living matter.

Hydrocarbons - Organic molecules consisting only of carbon and hydrogen. Hydrocarbons are the major components of petroleum. Petroleum is a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago.

Hydrocarbon molecules are found in living organism attached to non-hydrocarbon components - Fats.

Fats and petroleum are hydrophobic compounds because the bonds between the carbon and hydrogen atoms are nonpolar. Hydrocarbons store a relatively large amount of energy. The gasoline that fuels a car consists of hydrocarbons, and the hydrocarbon tails of fat molecules serve as stored fuel for animal bodies.

Isomers - Compounds that have the same molecular formula but different structures and hence different properties (see figure 4.6 - page 56).

Structural isomers differ in the covalent arrangement of their atoms. The numbers of possible isomers increase tremendously as carbon skeletons increase in size.

Geometric isomers have the same covalent partnerships but they differ in their spatial arrangements. The inflexibility of double bonds will not allow the atoms they join to rotate freely about the bond axis.

The subtle difference in shape between geometric isomers can dramatically affect the biological activities of organic molecules.

Enantiomers are molecules that are mirror images of each other. A cell can distinguish these isomers based on their different shapes. Usually, one isomer is biologically active and the other is inactive. Enantiomers are important to the pharmaceutical industry because the two Enantiomers of a drug may not be equally effective. In some cases the isomers can have a harmful effect.

The distinctive properties of an organic molecule depend not only on the arrangement of its carbon skeleton, but also on the molecular components attached to that skeleton.

Functional Groups - The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups. Each functional group behaves consistently from one organic molecule to another, and the number and arrangement of the groups help give each molecule its unique properties (see figure 4.8 - page 57). In the case of testosterone vs. estradiol, male and female sex hormones. Both are steroids, organic molecules with a common carbon skeleton in the form of four fused rings. These sex hormones differ mainly in the functional groups attached to the rings. The different actions of these two molecules on many targets throughout the body help produce the contrasting features of females and males.

The six functional groups most important in the chemistry of life are the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups. All are hydrophilic and thus increase the solubility of organic compounds in water (see table 4.1 - page 58).

Hydroxyl group - A hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. Organic compounds containing hydroxyl groups are called alcohols, and their specific names usually end in - ol (ethanol). The hydroxyl group is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Consequently, water molecules are attracted to the hydroxyl group, and this helps dissolve organic compounds containing such groups.

Sugars owe their solubility in water to the presence of multiple hydroxyl groups.

Carbonyl group - Consists of a carbon atom joined to an oxygen atom by a double bond. If the carbonyl group is on the end of a carbon skeleton, the organic compound is called an aldehyde; otherwise the compound is called a ketone. The simplest ketone is acetone, which is three carbons long. Acetone has different properties from propanal, a three carbon aldehyde. The variation in location of the functional group along the carbon skeleton is a major source of molecular diversity.

Carboxyl group - When an oxygen atom is double bonded to a carbon atom that is also bonded to a hydroxyl group. Compounds containing carboxyl groups are known as carboxylic acids, or organic acids. A carboxyl group is a source of hydrogen ions, which gives this group its acidic properties. The covalent bond between the oxygen and the hydrogen is so polar that the hydrogen tends to dissociate reversibly from the molecule as an ion (H+).

Amino group - Consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. Glycine is both an amine and a carboxylic acid. Its molecule has both a carboxyl group and an amine group. Most of cell’s organic compounds have two or more different functional groups. Glycine and similar compounds having both amino and carboxyl groups are called amino acids; these are the molecular building blocks of proteins.

Sulfhydryl group - Consists of a sulfur atom bonded to an atom of hydrogen (-SH), resembling a hydroxyl group in shape. Organic compounds containing sulfhydryls are called thiol.

Phosphate group - Have a phosphate ion covalently attached by one of its oxygen atoms to the carbon skeleton. One function of phosphate groups is the transfer of energy between organic molecules.

(See The chemical elements of life: a review - page 59)

Water and the Environment Chapter 3

The abundance of water is a major reason the Earth is habitable. “For life to exist at all, the environment must first be a suitable abode. Water is the only common substance to exist in the natural environment in all three physical states of matter: solid, liquid and gas. Water is the biological medium here on Earth, and possibly on other planets as well.

Water is a polar molecule - 1 oxygen atom is covalently bonded to 2 separate hydrogen atoms. These bonds complete the valence shells of all 3 atoms. Since the oxygen atom has a higher electronegative charge, the hydrogen electrons are pulled closer to the oxygen atom giving it a net negative charge (-) and the hydrogen atoms end up with a slightly positive charge (+). Opposite ends of the molecule have opposite charges. A molecule having a (+) charge can be attracted to the (-) charge of the oxygen atom, and (-) charged molecules can be attracted to the (+) charge of the hydrogen atoms -

hydrogen bonding.

Each water molecule can form hydrogen bonds to a maximum of four neighbors. The extraordinary qualities of water are emergent properties resulting from the hydrogen bonding that orders molecules into a higher level of structural organization.

Four of water’s properties that contribute to the living environment are: water’s cohesive behavior, its ability to stabilize temperature, its expansion upon freezing, and its versatility as a solvent.

Cohesion - Water molecules stick to each other as a result of hydrogen bonding. These bonds are weaker than covalent bonds. They form, break and re-form with great frequency. Each bond only last a trillionth of a second, but the molecules are constantly forming new bonds with a succession of partners. At any instant, a substantial percentage of all the water molecules are bonded to their neighbors making water more structured than most other liquids. Collectively, the hydrogen bonds hold the substance together. This is called

cohesion. Cohesion due to hydrogen bonding contributes to the transport of water against gravity in plants.

Adhesion - The clinging of one substance to another. Adhesion of water to the walls of the vessels in plants helps counter the downward pull of gravity.

Surface Tension - A measure of how difficult it is to stretch or break the surface of a liquid. Water has a greater surface tension than most liquids. Some animals and insects can stand, walk, or run on water without

breaking the surface (see diagram - page 43).

Water moderates temperatures on Earth - Water stabilizes temperatures by absorbing heat from air that is warmer and releases the stored heat to air that is cooler. Water can absorb or release a relatively large amount of heat with only a slight change in its own temperature.

Kinetic energy - The energy of motion. Atoms and molecules have kinetic energy because they are always moving. The faster a molecule moves, the greater its kinetic energy.

Heat - Is the measure of the total quantity of kinetic energy due to molecular motion in a body of matter.

Temperature - Measures the intensity of heat due to the average kinetic energy of the molecules.

When the average speed of the molecules increases, a thermometer records this as a rise in temp.

Heat and temperature are related but not the same. Whenever 2 objects of different temperature are brought together, heat passes from the warmer to the cooler body until the two objects are the same temp.

Celsius Scale - 0oC = 32oF = freezing point of water 100oC = 212oF = boiling point of water

Average temp. of the human body = 37oC = 98.6oF

Average room temp. = 20 - 25oC = 68 - 77oF

C = F x 9 / 5 + 32 F = (C - 32) x 5 / 9

Calorie - A calorie is the amount of heat energy it takes to raise the temperature of 1 gram of water by 1oC.

A calorie (cal) is also the amount of heat that 1 g of water releases when it cools by 1oC.

A kilocalorie (kcal), 1,000 cal, is the quantity of heat required to raise the temperature of 1 kilogram (kg) of water by 1oC. “Calories” on food packages are actually kilocalories.

Joule - One joule (J) = 0.239 cal 1 cal = 4.184 J

Specific Heat - The amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1oC. The specific heat of water is 1 calorie per gram per degree Celsius - 1 cal/g/oC.

Compared to most other substances, water has an unusually high specific heat. The ability of water to stabilize temperature stems from its relatively high specific heat.

Because of the high specific heat of water relative to other materials, water will change its temp. less when it absorbs or loses a given amount of heat. Specific heat can be thought of as a measure of how well a substance resists changing its temp. when it absorbs or releases heat. Water absorbs or loses a relatively large quantity of heat for each degree of change. Water’s high specific heat is a result of it hydrogen bonding. Heat must be absorbed in order to break hydrogen bonds, and heat is released when hydrogen bonds form.

Relevance to life on Earth - A large body of water can absorb and store a huge amount of heat from the sun in the daytime and during summer, while warming up only a few degrees. At night and during winter, the gradually cooling water can warm the air. The high specific heat of water also tends to stabilize ocean temps., creating a favorable environment for marine life. The water that covers the Earth keeps temperature fluctuations on land and in water within the limits that permit life. Also, because organisms are made primarily of water, they are more able to resist changes in their own temperatures than if they were made of a liquid with a lower specific heat.

Molecules of any liquid stay close together because they are attracted to one another. Molecules moving fast enough to overcome these attractions can depart the liquid and enter the air as gas. This transformation from a liquid to a gas is called vaporization, or evaporation. If a liquid is heated, the average kinetic energy of molecules increases and the liquid evaporates more rapidly.

Heat of vaporization - The quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state. Water has a high heat of vaporization. To evaporate one gram of water at 25oC, about 580 cal of heat is needed - nearly double the amount needed to vaporize a gram of alcohol or ammonia.

Evaporative Cooling - As a liquid evaporates, the surface of the liquid that remains behind cools down because the “hottest” molecules (those with the greatest kinetic energy) are the most likely to leave as gas.

Evaporative cooling contributes to the stability of temperature in lakes and ponds and also provides a

mechanism that prevents terrestrial organisms from overheating (sweat).

Water is one of the few substances that are less dense as a solid than as a liquid. Ice floats. While other materials contract as they solidify, water expands. Water begins to freeze when its molecules are no longer moving vigorously enough to break their hydrogen bonds. As the temperature reaches 0oC, the water becomes locked into a crystalline lattice, each water molecule bonded to the maximum of four other molecules. These bonds are far enough apart to make ice about 10% less dense than liquid water at 4oC. Liquid water is most dense when its temp. is 4oC. At higher temps it expands because the molecules will be moving faster. The hydrogen bonds in ice are stable. When in the liquid state, the hydrogen bonds constantly break and reform.

The ability of ice to float because of the expansion of water as it solidifies is an important factor in the fitness of the environment. If ice sank, then eventually all lakes, ponds, and oceans would freeze solid making life impossible. When a deep body of water cools, the floating ice insulates the liquid water below, preventing it from freezing and allowing life to exist under the frozen surface.

Solution - A liquid that is a completely homogeneous mixture of two or more substances.

Solvent - The dissolving agent of a solution.

Solute - The substance that is dissolved in a solution.

Sugar placed in a glass will dissolve. The glass will then contain a uniform mixture of sugar and water; concentration of dissolved sugar will be the same everywhere in the mixture. This is called a solution. The sugar is the solute. The water is the solvent.

When the solvent of a solution is water it is called an aqueous solution.

Because the water molecule is polar, it becomes attracted to the ions of the solute causing bonds in the ion to break and reform with the oxygen or hydrogen of the water molecule. In the case of sodium chloride, table salt, the oxygen regions are negatively charged and cling to the positively charged sodium cations. The hydrogen regions of the water molecule are positively charged and are attracted to the negatively charged chloride anions. As a result, water molecules surround the individual sodium and chloride ions on the surface of the sodium chloride crystal, separating and shielding them from one another. The sphere of water molecules around each dissolved ion is called a hydration shell. Working inward from the surface of the salt crystal, water eventually dissolves all the ions. The result is a solution of two solutes, sodium and chloride, homogeneously mixed with water (see page 45-46).

Compounds made up of polar molecules, such as sugars, are also water-soluble (dissolve). Such compounds dissolve when water molecules surround each of the solute molecules. Even proteins can dissolve in water if they have ionic and polar regions on their surface.

Many different kinds of polar compounds are dissolved (along with ions) in the water of such biological fluids as blood, the sap of plants, and the liquid within all cells. Water is the solvent of life.

Hydrophilic - (Greek - hydro = water, and philios = loving) Any substance that has an affinity for water even if the substance does not dissolve. Cotton absorbs water without dissolving. The giant molecules of cellulose (a compound with numerous regions of partial positive and partial negative charges associated with polar bonds. Water adheres to the cellulose fibers. Cellulose is also present in the walls of water- conducting vessels in a plant.

Hydrophobic - (Greek - hydro = water, and phobos = fearing) Substances that do not have an affinity for water. Substances that are non-ionic and nonpolar seem to repel water. Vegetable oil does not mix with water. The hydrophobic behavior of the oil molecules results from the prevalence of non-polar bonds between carbon and hydrogen which share electrons almost equally. Hydrophobic molecules related to oils are major ingredients of cell membranes. Without this property, cells would dissolve and life would not be able to exist.

Molecular Weight - The sum of the weights of all the atoms in a molecule.

Table sugar - sucrose (C12H22O11)

C=12 daltons, H=1 dalton, O=16 daltons - molecular weight = 342 daltons

Mole - Is equal in number to the molecular weight of a substance but scaled from daltons to units of grams.

1 mole of sugar is equal to 342 grams. The number of molecules in a mole is 6.02 x 1023.

This number is referred to as Avogadro’s number. All substances have the same amount of molecules per mole but the molecular weight may be different. (page 46)

Dissociation of Water Molecules - Occasionally, a hydrogen atom shared by two water molecules in a hydrogen bond shifts from one molecule to the other. When this happens, the hydrogen atom leaves its electron behind, and what is actually transferred is a hydrogen ion (H+), a single proton with a charge of +1. The water molecule that lost a proton is now a hydroxide ion (OH-), which has a charge of -1. The proton binds to the other water molecule, making that molecule a hydronium ion (H3O). The dissociation of water is reversible and statistically rare, it is exceedingly important in the chemistry of life.

Hydrogen and hydroxide ions are very reactive. Changes in their concentrations can dramatically affect a cell’s proteins and other complex molecules. The concentrations of H+ and OH- are equal in pure water, but adding certain kinds of solutes called acids and bases disrupts this balance.

pH Scale - A scale to describe how acidic or basic a solution is. An acid is a substance that increases the hydrogen ion (H+) concentration of a solution. As the acid dissolves in water H+ ions are added to the solution and lowers the pH. We say the solution is more acidic. (see page 47)

A substance that reduces the hydrogen ion concentration of a solution is called a base. A base reduces the amount of H+ and increases the amount of hydroxide ions (OH-). We say the solution become increasingly basic. When the concentration of H+ and OH- are equal the solution is neutral.

The pH scale is a range is a range of 0 - 14. The lower the number, the more acidic, 7 is neutral and the higher numbers are more basic. (see scale on page 48) Each increase or decrease in number on the scale represents a tenfold difference in the amount of H+ or OH-. Strong acidity can alter the structure of biological molecules and prevent them from carrying out the essential chemical processes of life.

Buffers are substances that minimize changes in the concentrations of H+ and OH- in a solution. Buffers work by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to the solution when the have been depleted. Most buffer solutions contain a weak acid and its corresponding base. In human blood, carbonic acid (H2CO3) acts as a buffer to maintain the stability of pH within the blood. Carbonic acid dissociates to yield a bicarbonate ion (HCO3-) and a hydrogen ion (H+). Bicarbonate and carbonic acid act as a pH regulator, the reaction shifting left or right as other processes in the solution add or remove hydrogen ions.

Biology Notes

Atoms/Elements/Molecules/Compounds Chapter 2

Matter - Organisms are composed of matter which is anything that takes up space and has mass. Matter exists in many diverse forms, each with its own characteristics. Matter consists of chemical elements in pure form and in combinations called compounds.

Elements - An element is a substance that cannot be broken down to other substances by chemical reactions. There are 92 recognized naturally occurring substances (hydrogen, oxygen, helium) 118 in all.

Compounds - A substance consisting of two or more elements combined in a fixed ratio.

Table salt is made of sodium chloride (NaCl). Pure sodium is a metal and pure chlorine is a poisonous gas. Chemically combined, however, sodium chloride is an edible substance that has completely different characteristics than the elements that made it.

About 25 of the 92 naturally occurring elements are essential to life. Carbon (C), oxygen (O), hydrogen (H) and nitrogen (N) make up 96% of living matter. (See table 2.1 pg 28)

Atoms - The smallest unit of matter that still retains the properties of an element. Each element consists of a certain kind of atom that is different from the atoms of any other element. The properties of elements and of the compounds they form ultimately result from the structure of atoms.

Atoms are symbolized with the same abbreviation used for the element made up of those atoms; thus, C stands for both the element carbon and a single carbon atom.

Atoms are composed of subatomic particles, 3 of which will be relevant to biology - protons, neutrons and electrons. Protons and neutrons are packed together tightly to form a dense core (atomic nucleus), at the center of the atom. The electrons, moving at nearly the speed of light, form a cloud around the nucleus.

Electrons and protons are electrically charged. Electrons are negatively charged (-) and protons are positively charged (+). Each has one unit of charge. Neutrons are electrically neutral. Protons give the nucleus a positive charge and it is the attraction between opposite charges that keeps the rapidly moving electrons in the vicinity of the nucleus.

Protons and neutrons are almost identical in mass, each about 1.7 x 10-24 grams and electrons are 1/2000 the mass of the protons and neutrons. Since these numbers are so small, scientists use the dalton (in honor of John Dalton, British scientist who helped develop atomic theory around 1800) as the unit of measure for atomic mass for atoms and subatomic particles. Since the electron’s mass is so small it does not figure into the atomic mass. Neutrons and protons have masses close to 1 dalton.

The configuration of how many protons, neutrons and electrons an atom has determines the characteristics of the atom/element. All atoms of a particular element have the same number of protons in their nuclei.

Atomic Number - Written as a subscript to the left of the symbol for an element, the atomic number is the number of protons in the nucleus. Examples - 2He (helium), 3Li (lithium) and 8O (oxygen).

Unless otherwise indicated, an atom is neutral in electrical charge, which means that its protons must be balanced by an equal number of electrons. Therefore, the atomic number tells us the number of protons and electrons in an electrically neutral atom.

Atomic Mass - Written as a superscript to the left of the symbol for an element, the atomic mass is the sum of the protons plus neutrons in the nucleus of an atom. Examples - 42He and 4822Ti (titanium)

An atom of titanium has 22 protons, 22 electrons and 26 neutrons.

Atomic Weight - Neutrons and protons each have a mass very close to 1 dalton, therefore, the mass number is an approximation of the total mass of an atom, referred to as the atomic weight. The atomic weight of helium is approx. 4 daltons. Electrons are so small that they don’t contribute to the atomic weight.

Isotope - All atoms of a given element have the same number of protons, but some atoms have more neutrons than other atoms of the same element and therefore weigh more. These different atomic forms are referred to as isotopes of the element. 126C, 136C and 146C are isotopes of Carbon. All the atoms have 6 protons but the last two have 7 and 8 neutrons respectively. 14C is radioactive, meaning the nucleus is unstable and decays giving off particles and energy. When the decay leads to a change in the number of protons, it transforms the atom to an atom of a different element. Carbon decays to form nitrogen.

Radioactive decay is used in the process of dating fossils and can be used to trace systems in the body to determine or monitor chemical processes in the body (See page 30 figure 2.7).

Energy - the ability to do work.

Potential Energy - the energy that matter stores because of its position or location. Water in a reservoir on a hill has potential energy. When the gates of the reservoir’s dam are opened and the water runs downhill, the energy comes out of storage to do work, such as turning generators to produce electricity. Because potential energy has been expended, the water stores less energy at the bottom of the hill than it did in the reservoir at the top of the hill.

Matter has a natural tendency to move to the lowest possible state of potential energy. To restore the potential energy of a reservoir, work must be done to elevate the water against gravity.

Electrons of an atom have potential energy because of their position in relation to the nucleus. The negatively charged electrons are attracted to the positively charged nucleus; the more distant the electrons are from the nucleus, the greater their potential energy. There is a greater potential to interact with other atoms or to move to a different electron shell.

Electron Shells/Energy Levels - are the different states of potential energy that electrons have in an atom. The first shell is closest to the nucleus, and electrons in this shell have the lowest energy. Electrons in the 2nd shell have more potential energy; electrons in the 3rd shell have more energy still, and so on. An electron can change its shell, but only by absorbing or losing an amount of energy equal to the difference in potential energy between the old shell and the new shell. To move to a shell closer to the nucleus, an electron must lose energy, which is usually released to the environment in the form of heat.

The chemical behavior of an atom is determined by it electron configuration - the distribution of electrons in the atom’s electron shells and mostly on the number of electrons in the outermost shell called the valence shell. The electrons in the valence shell are called the valence electrons.

The Periodic Table is organized by how the valence shells of the different elements. The first row has one valence shell, the 2nd row has two, and so on (See diagram on page 32).

Orbitals - The three-dimensional space where an electron is found is called its orbital. No more than 2 electrons can occupy the same orbital. The first orbital shell of any atom (closest to the nucleus) can only have 2 electrons in the orbital. Hydrogen has 1 and helium has 2. The second orbital shell has 4 orbitals which can contain up to 2 electrons/orbital for a total of 8 electrons.

The amount of electrons per orbital follows the formula 2n2.

1st orbital - 2(1)2 = 2 2nd orbital - 2(2)2 = 8 3rd orbital - 2(3)2 = 18 4th orbital 2(4)2 = 32

This formula holds true for the first 4 levels.

Covalent Bonds - When 2 or more atoms share electrons from there valence shell to complete the number of electrons allowed for that orbital. When the atoms of the same element share electrons they form a molecule of that element. A molecule is defined as two or more atoms held together by covalent bonds.

H-H 2 hydrogen atoms can share their electrons to complete the valence shell.

O-O 2 oxygen atoms share 2 electrons to form a double covalent bond.

Non-polar covalent bond - when atoms share electrons equally

Polar covalent bond - when one atom has a stronger electronegative charge and has a greater attraction to the shared electrons from the other atom. Oxygen has a stronger attraction to the electrons it shares with hydrogen. This gives oxygen a slight negative charge and the hydrogen ends up with a positive charge. Water is a polar molecule. Opposite ends of the molecule have opposite charges.

Ionic bond - when an atom’s electron is taken by another atom to complete its valence shell. The atom that lost the electron now has a net positive charge (positive ion + cation) and the receiving atom with the extra electron has a net negative charge (negative ion - anion). Ions with opposite charges attract one another.

Na (sodium) and Cl (chlorine) form sodium chloride (NaCl) - table salt. Compounds formed by ionic bonds are called ionic compounds or salts

Hydrogen bonds - form when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom. Remember, when hydrogen is covalently bonded to another atom it has a slight positive charge. Hydrogen in a water molecule (H2O) with a + charge can be attracted to a - charged nitrogen atom of an ammonia molecule (NH3) (See diagram on page 36). This is a weaker bond than a covalent bond.

Weak bonds between molecules within the cells of organisms is extremely important. When two molecules in the cell make contact, they may adhere temporarily by types of chemical bonds that are weaker than covalent bonds. The advantage of weak bonding is that the contact between the molecules can be brief; the molecules come together, respond to one another in some way and then separate.

Example: chemical signaling in the brain between receiving cells and signaling cells.

Molecular shape is crucial in biology because it determines how most biological molecules recognize and respond to one another. The unique shape of some molecules allow them to fit like a key into receptor cells to cause a response.

Chemical reactions make and break chemical bonds - The making and breaking of chemical bonds, leading to changes in the composition of matter, are called chemical reactions.

2 H2 + O2 = 2 H2O 2 sets of hydrogen atoms covalently bonded chemically react with 2 oxygen atoms covalently bonded to form 2 water molecules.

The starting material is called the reactants and the end result material is the product. All atoms of the reactants must be accounted for in the products. Matter is conserved in a chemical reaction. Chemical reactions cannot create or destroy matter but can only rearrange it.

6 CO2 + 6 H2O ---- C6H12O6 + 6 O2 (photosynthesis)

Most chemical reactions can be reversed. Reactants bond to form products and the products can be broken back down into the reactants.

One of the factors affecting the rate of reactions is the concentration of reactants. The greater the concentration of reactant molecules, the more frequent they collide with one another and have an opportunity to react to form products. As products accumulate, collisions resulting in the reverse reaction become increasingly frequent. Eventually, the forward and reverse reactions occur at the same rate, and the relative concentrations of product and reactants stop changing. The point at which the reactions offset one another exactly is called chemical equilibrium. Reactions continue to occur but with no net effect on the concentrations of reactants and products.

Biology Notes

Introduction to Biology Chapter 1

What is Biology: The study of living organisms. Biology is a multidisciplinary science that incorporates chemistry, physics and mathematics as well as the humanities and social sciences. Life is complex, from atoms to molecules, compounds to cells, organs to systems, reproduction and inheritance, living organisms to their interactions with the environment.

Themes:

1. Emergent Properties - The living world has a hierarchical organization. With each step upward in organizational level, novel properties emerge as a result of interactions among components at the lower levels.

Example - A heart is an organ made up of smaller units that have their own characteristics. Individually these cells are not a heart but put together as many different tissues you have an organ that has its own function within a larger network called the circulatory system.

Hierarchical Structure - Atoms are the fundamental chemical building blocks to all matter.

Atoms are ordered into complex biological molecules.

Many of the molecules of life are arranged into minute structures called organelles.

Organelles are the components of cells.

Cells are subunits of organisms.

Organisms are the units of life.

2. The Cell - Every organism’s basic units of structure and function is the cell. There are two types of cells, prokaryotic cells in bacteria and archaea and eukaryotic (much more complex with internal substructures) cells in protists, plants, fungi and animals.

3. Heritable information - The continuity of life depends on the inheritance of biological information in the form of DNA molecules. This genetic info is encoded in the nucleotide sequences of the DNA (deoxyribonucleic acid). Order implies information and instructions are required to arrange parts or processes in an organized way. Example - to bake a cake one needs a list of ingredients and instructions on how to combine these ingredients and bake them at a certain temp to have a finish product that one can eat as a cake.

DNA is the substance of genes, the units of inheritance that transmit information from parent to offspring.

4. Structure/Function - Analyzing a biological structure gives us clues about what it does and how it works. Conversely, knowing the function of a structure provides insight about its construction. How a device works is correlated with its structure. Example - You would not loosen a screw with a hammer or drive a screw with a screwdriver. The infoldings of membrane in the mitochondrion make it a perfect structure for cell respiration.

5. Interaction with environment - Organisms are open systems that interact continuously with the environment. Organisms exchange materials and energy with its surroundings. Interaction with the environment includes living as well as nonliving factors.

6. Regulation - Feedback mechanisms regulate biological systems. Many biological processes are self-regulating in which the output or product of a process regulates that process. Positive and negative feedback speed up or slow down biological processes.

7. Unity and diversity - Biologists group the diversity of life into three domains: Bacteria, Archaea, and Eukarya, based on their cellular structure/function. Bacteria and Archaea are mostly unicellular organisms with prokaryotic cells. The Eukarya domain consists of organisms with eukaryotic cells and is divided into 4 kingdoms (Protista, Plantae, Fungi and Animalia).

Protista - unicellular and simple multicellular eukaryotes.

Plantae - multicellular eukaryotes that carry out photosynthesis.

Fungi - multicellular eukaryotes that absorb nutrients from decomposing organic material.

Animalia - multicellular eukaryotes that ingest other organisms.

As diverse as life is, we can also find unity, such as a universal genetic code, DNA. The more closely related two species are, the more characteristics they share.

8. Evolution - Biology’s core theme, explains both the unity and diversity of life. The Darwinian theory of natural selection accounts for adaptation of populations to their environment through the differential reproductive success of varying individuals. Evolution is the process that has transformed life on Earth from its earliest beginnings to the extensive diversity we see today.

Charles Darwin published The Origin of Species in 1859. He presented 2 main concepts, that contemporary species arose from a succession of ancestors through a process of “descent with modification” and life evolves through a process of natural selection. The differential reproductive success of those individuals with traits best suited to the local environment generally leave a disproportionately large number of surviving offspring. This differential reproductive success of some individuals over others means that certain heritable traits are more likely to appear in each new generation. Darwin called differential reproductive success natural selection, and he envisioned it as the cause of evolution. Darwin travelled the world on a five year voyage on the HMS Beagle (December, 1831- October 1836).

9. Scientific inquiry - The process of science includes observation-based discovery and the testing of explanations through hypothetico-deductive method. Scientific credibility depends on the repeatability of observations and experiments. Scientific Method:

Observations

Question

Hypothesis

Prediction

Test/Experiment

Theory

10. Science, technology and society - Many technologies are goal-oriented applications of science. Science catalyzes certain technologies by complementing trial and error with more informed design. But the direction technology takes depends less on science than it does on the needs of humans and the values of society.

Levels of biological organization - A level of biological organization represents a certain degree of size and complexity of body structures, as well as the inter-relationships between them and other non-body structures. In biology, a Pyramid of Life can be identified. There are 12 levels with the least complex at the bottom and the most complex at the top. Level 12 at the top contains all the other levels of biological organization below and within it. Further, each of the other levels likewise contains the lower levels closer to the broad base of the pyramid. The farther one goes up in the Pyramid, the greater the size and complexity of the biological patterns encountered.

1. Subatomic Particles

2. Atoms

3. Molecules

4. Organelles

5. Cells

6. Tissues

7. Organs

8. Organ Systems

9. Organisms

10. Population

11. Community

12. Ecosystem
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