Unit One

1. Unit One Science Basics & Chemistry of Living Things

2. Science Basics • The Scientific Method – a series of steps used to learn new information about a specific topic; usually consists of five steps • 1. State Problem • 2. Formulate Hypothesis • 3. Experiment • 4. Analyze Results • 5. Make Conclusion

3. Science Basics Hypothesis – educated guess (usually very little previous knowledge on the topic) Theory – statement/idea based on a large body of supporting evidence Scientific Law – accepted as fact by the scientific community The only way scientific thought is advanced is through objective unbiased experimentation

4. Matter and the Elements Matter is anything that has mass and takes up space An Element is a pure form of matter that cannot be broken down into a simpler form An Atom is the smallest unit of any element that still retains the physical and chemical properties of said element An atom consists of three subatomic particles: Protons, Neutrons, and Electrons

5. More about the Atom At the center of an Atom is the Nucleus The Nucleus contains both Protons and Neutrons Electrons orbit around the nucleus in pathways that are not very well defined; they are referred to as orbitals and/or shells Protons are positive (+), Electrons are negative (-), and Neutrons have no charge

6. More about the Atom Protons and Neutrons are much more massive than Electrons It can be stated that the mass of an Atom is due almost entirely to the presence of Protons and Neutrons (the mass of Electrons is negligible) Due to the above fact, Atomic Mass/Mass Number takes into account the mass of Protons and Neutrons Atomic Number is the total number of Protons in an Atom

7. The Periodic Table of the Elements A systematic chart used to assist in the study of chemical reactions between Atoms and Molecules Initially developed by Mendeleev (Russian) in the late 1800’s; his chart organized Elements by Atomic Mass http://www.aip.org/history/curie/periodic.htm It was later determined the best way to organize Elements was via Atomic Number

8. More on the Periodic Table Each Element has a Shorthand Representation that consists of either one or two letters: Sulfur S Neon Ne A row is called a Period and a column is called a Group Elements are listed from left to right by ascending Atomic Number There are three categories of elements: Metal, Metalloid, & Nonmetal http://www.chemicalelements.com/

9. Basic Chemistry How an atom interacts with other atoms is determined by the electrons; therefore, the chemical behavior of the atom is due to the actions of the electrons All atoms seek to be chemically stable by attempting to obtain 8 electrons in their outer shell called the Valence Shell Those “pathways” mentioned earlier are areas in which the electrons travel while orbiting the nucleus. The pathways are often referred to as Orbitals In order for an atom to achieve the desired chemical stability it will attempt to either gain or lose electrons from the orbitals of the valence shell

10. Helium

11. Carbon

12. Basic Chemistry The orbitals in which electrons are commonly found are the “S”, “P”, “D”, and “F” The S orbital can have up to 2 electrons The P orbital can have up to 6 electrons The D orbital can have up to 10 electrons The F orbital can have up to 14 electrons

13. Ions Atoms in which the number of electrons does not equal the number of protons are Ions If an atom has fewer electrons than protons it is positively charged (the + protons outnumber the – electrons); these are called Cations If an atom has more electrons than protons it is negatively charged (the –electrons outnumber the + protons); these are called Anions He+ (cation), Cl- (anion)

14. Isotopes Atoms of an element that have different numbers of neutrons are called Isotopes Isotopes of an atom of a specific element have the same atomic number (# of protons) but different mass number (protons + neutrons) Radioactive Isotopes are used in medicine to detect and treat cancer, and they are used to determine the approximate age of fossils

15. Molecules • A Molecule is a group of atoms held together by the energy of interacting electrons • There are 2 categories of bonds that electrons form when interacting with eachother: • Ionic Bonds – unequal sharing of e- • Covalent Bonds – equal sharing of e- • Because covalent bonds involve the sharing of electrons, single, double, and triple bonds exist in order to optimize the presence of the electrons in an attempt to fill the valence shell of each atom

16. Molecules The atoms of most inorganic (nonliving) substances form ionic bonds, whereas, the atoms of most organic (living) substances form covalent bonds Examples of elements which are commonly found in organic substances are: Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus Examples of elements which are commonly found in inorganic substances are: Aluminum, Chlorine, Lead, Silver, and Gold

17. Molecules Hydrogen bonds are weak chemical bonds that play a special role in biology Two key properties of hydrogen bonds cause them to play an important role in biological molecules: they are weak, and as a result of their weakness, they are highly directional The bottom line is that hydrogen bonds stabilize the shapes of many important biological molecules

18. Water and Hydrogen Bonds Polar molecules other than water are called Hydrophilic because they are attracted to the hydrogen bonds of water Nonpolar molecules are called Hydrophobic because they are repelled by the hydrogen bonds of water If polar molecules dissolve in water they are Soluble

19. Water Formulas • The Chemical Formula for water is H2O • The Structural Formula for water is:

20. Ionization of Water • Water can be broken apart into two ions: • H+ and OH- • H+ is a Hydrogen Cation • OH- is a Hydroxide Anion • H+ equals acidic • OH- equals basic • The way to measure the acidity or basidity of a substance is by using the pH scale

21. pH Scale – “Percentage of Hydrogen” The scale ranges from 0 to 14 O to 6.9 is acidic, with 1 and 2 being very acidic 7 is neutral (neither acidic or basic) 7.1 to 14 is basic, with 13 and 14 being very basic Again, if there are many hydroxide anions (OH-) in solution, then the solution is basic If there are many hydrogen cations (H+) in solution, then the solution is acidic

22. pH Scale

23. pH Scale and Buffers In order to change the pH of a solution, a buffer can be added A buffer is a solution of known pH that can lower or raise the pH of the solution in question Buffers do the above by either absorbing or releasing H+ cations into solution Buffers are important in that they keep solutions from becoming too acidic or too basic; buffers keep solutions’ pH in an acceptable range

24. Monomers and Polymers Organic Molecule – a molecule formed by living organisms that consist of a carbon backbone with other elements bonded to it All four categories of macromolecules, which are organic, are made from monomers that combine to form polymers Macromolecules – very large molecules that are necessary for the maintenance of the structure and function of the cell Monomer – a subunit or “train car” that when connected to others forms a polymer or “train”

25. Monomers and Polymers • Polymer – a large molecule composed of many subunits (“train cars”) • All four categories of macromolecules connect their monomers (subunits) in the same way: • “Dehydration Synthesis” – making polymers from monomers • OH group is removed from one subunit and an H group is removed from the other subunit • Both the OH and H groups together compose water (H2O); this is why this process is called “Dehydration” • An enzyme (protein) is used to facilitate this reaction

26. Monomers and Polymers • To breakdown a polymer the opposite of Dehydration Synthesis occurs and is called “Hydrolysis” • Hydrolysis – reducing a polymer to its monomer parts • An OH and H group are added to opposite sides of a subunit , therefore causing the polymer to be broken into its monomer parts

27. Proteins Monomer = Amino Acid Polymer = Protein 20 common amino acids which differ by their functional group Amino Acids are linked by “Peptide Bonds”(a type of covalent bond), and are formed via Dehydration Synthesis Long chains of amino acids linked by Peptide Bonds are called “Polypeptides”

28. Proteins • The way in which proteins function is determined by the shape of the protein, which in turn, is determined by what monomers bond with each other • There are four levels of protein structure that determine functionality: • Primary – long chain • Secondary – long chain folds • Tertiary – long chain folds and twists • Quaternary – more than one polypeptide chain

29. Proteins Proteins can only function in a specific range in reference to temperature and pH If the temperature is too high, or the environment is too acidic (low pH), then the protein unfolds and no longer functions = “Denatured” Proteins are extremely important because they serve as the “local government”: they ensure the proper function of the cell Tertiary Proteins are Enzymes Enzymes act as catalysts, which govern cellular reactions

30. Proteins

31. Nucleic Acids Monomer = Nucleotide Polymer = Nucleic Acid (RNA & DNA) The 5 Carbon Sugars of each Nucleotide are linked by Phosphate Groups to form Polynucleotide Chains = RNA and DNA RNA is found in viruses, and both RNA and DNA are found in other species RNA is single-stranded DNA is double-stranded

32. Nucleic Acids Polynucleotide Chains (RNA and DNA) function is essentially that of a library: these macromolecules possess all the information necessary to both form an individual and maintain that individual throughout life

33. Nucleic Acids

34. Carbohydrates • Monomer = Simple Carbohydrate • Polymer = Complex Carbohydrate • Carbohydrates purpose is to serve as an energy supply for cells, and in some cases (polysaccharides), to serve as a structural support to organelles in cells • Simple Carbohydrates • Monosaccharides – one monomer/subunit, Glucose is an example C6H12O6 • Disaccharides – two monomers/subunits linked together via dehydration reaction, Lactose is an example

35. Carbohydrates • Complex Carbohydrates • Polysaccharides – long polymer chains; Starch, Glycogen, Chitin, and Cellulose • Starch (plants) and Glycogen (animals) are storage macromolecules for energy when energy is not immediately needed by the organism’s cells • Cellulose (plants) and Chitin (animals) are carbohydrate macromolecules that assist with structural support of organelles within the organism’s cells

36. Carbohydrates“Glucose”

37. Lipids Monomer = Fatty Acids and Glycerol Polymer = Lipid or “Triglyceride” Lipids are “Fats” They are not soluble in water because of the chemistry of their structure They are soluble in oil Lipids are composed primarily of Carbon and Hydrogen atoms bonded to each other

38. Lipids Saturated Fat – each carbon is bonded to as many hydrogen atoms as is possible Unsaturated Fat – not every carbon is bonded to all hydrogens as is possbile, and therefore, double and triple bonds form between carbon atoms Lipids serve as long term energy storage for cells, and also serve as the primary component of all cells plasma membrane (barrier to outside world)

39. Lipids