The Chemical Level of Organization

1. Chapter 2 The Chemical Level of Organization

2. Atoms • Chemistry is the science that investigates matter and its interactions • Atoms are the basic particles of matter • Matter is anything that takes up space and has mass • Matter occurs in 3 states: solid, liquid, and gas • All matter is composed of elements which cannot be broken down or changed • The smallest, stable unit of matter is the atom

3. Atomic Structure • Atoms contain 3 types of subatomic particles: protons (positive electrical charge), neutrons (uncharged), and electrons (negative electrical charge) • Number of protons in an atom is its atomic number • Protons and neutrons are found in the nucleus, the center of the atom • Electrons orbit the nucleus forming the electron cloud (represented as a spherical electron shell)

5. Isotopes are atoms of a given element that differ in terms of the number of neutrons in the nucleus • Isotopes can only be distinguished from each other by their mass number (number of protons and neutrons in the nucleus) • Unstable isotopes are radioactive • Atomic weight is the average mass of an element’s atoms • Takes into account the mass of subatomic particles and relative proportions of any isotopes • Electrons are located in the electron shell • The number of electrons in an atom’s outer shell determines the chemical properties of that element • The first shell (ring) can contain 2 electrons and every ring after can contain up to 8 • If the outer ring is full then the atom is stable

6. Chemical Bonds • Chemical bonds are forces formed by atom interactions • The atoms most important to biology are the unstable ones because they interact and form larger structures • Bonding produces molecules (chemical structures with more than one atom bonded via sharing electrons) and compounds (chemical substances made up of atoms of 2 or more elements)

7. Chemical Bonds (cont.) • Ionic bonds • Ions are atoms or molecules with an electric charge (positive charge = cations and negative charge = anions) • Ionic bonds are chemical bonds created by the electrical attraction between anions and cations • Covalent bonds • A strong bond that involves the sharing of electrons • Can be single or double • Nonpolar covalent bonds = neutral bonds because of equal sharing • Polar covalent bonds = unequal sharing between atoms • Hydrogen bonds • Weak attraction between a slight positive charge on the hydrogen atom of one polar covalent bond and a weak negative charge on an O or N atom of another • Too weak to create molecules, but can alter shape and pull other molecules together

9. Decomposition, Synthesis, and Exchange Reactions • Cells stay alive by controlling chemical reactions • Chemical reactions are when new bonds are formed between atoms or when existing bonds are broken. • Basic energy concepts • Work is movement or change in the physical structure of matter • Walking or running • Energy is the capacity to perform work • There are 2 major types of energy: • Kinetic energy is energy in motion (falling) • Used to perform work • Potential energy is stored energy (stretched spring or charged battery) • Energy cannot be destroyed, it can only be converted • During each conversion some energy is released as heat (an increase in random molecular motion) • The temperature of an object is directly related to the average kinetic energy of its molecules • Heat can’t completely be converted to work or any other form of energy; cells can’t capture it or use it

10. Types of Reactions • Decomposition reactions • Breaks down a molecule into smaller fragments (digestion) • AB A + B • Decomposition reactions involving water are important in the breakdown of complex molecules in the body • Hydrolysis involves one of the bonds in a complex molecule being broken, and the components of a water molecule being added to the resulting fragments • A – B – C – D – E + H2O A – B – C – H + HO – D – E • Catabolism refers to the decomposition reactions of complex molecules within cells • Synthesis reactions • Synthesis is the opposite of decomposition; larger molecules are made from smaller components • A + B AB • Always involves the formation of new chemical bonds • Dehydration synthesis (condensation) is the formation of a complex molecule by the removal of water • A – B – C – H + HO – D – E A – B – C – D – E + H₂O • Anabolism is the synthesis of new compounds in the body • Exchange reactions • In an exchange reaction, parts of the reacting molecules are shuffled • AB + CD AD + CB

11. Reversible Reactions • Many important biological reactions are freely reversible • A + B AB • This equation means that 2 reactions are happening simultaneously, one synthesis and one decomposition • At equilibrium the rates of the 2 reactions are balanced

12. Enzymes and Activation Energy • Most chemical reactions do not occur spontaneously, or they occur so slowly that they are of no value to cells • For reactions to proceed, enough energy must be provided to activate the reactants • The amount of energy required to start to start a reaction is the activation energy • Cells use enzymes to speed up reactions that support life because cells can’t handle the harsh requirements reactions normally need • Enzymes are types of catalysts (compounds that accelerate chemical reactions without themselves being permanently changed) • Enzymes promote chemical reactions by lowering activation energy requirements • Lowering activation energy affects rate, not direction or products • Reactions absorb and release energy • Reactions that release energy are exergonic • Reactions that absorb energy are endergonic

14. Inorganic Compounds • Nutrients are essential elements and molecules obtained from the diet • Metabolites include all molecules synthesized or broken down by chemical reactions inside our bodies • Inorganic compounds are small molecules that generally do not contain carbon and hydrogen atoms • Water, carbon dioxide, oxygen, inorganic acids and bases, and salts • Organic compounds are mostly carbon and hydrogen atoms, they can be larger & more complex than inorganic compounds

15. Physiological Systems Depend on Water • Water is the single most important constitute of the body • 3 important general properties of water: • Water is an essential reactant in the chemical reactions of living organisms • Water has a very high heat capacity (the ability to absorb and retain heat) • Water is an excellent solvent

16. Body Fluid pH • pH is the concentration of hydrogen ions in a solution • It appears as a number between 0 and 14 • Water is a 7 = neutral • Below 7 is acidic and above 7 is basic (alkaline) • Blood and most bodily fluids normally range from 7.35 to 7.45 • Below 7 produces a coma and above 7.8 causes uncontrollable, sustained muscular contarctions

18. Acids, Bases, and Salts • An acid is any substance that breaks apart in solution to release hydrogen ions • Strong acids dissociate completely • Stomach acid • A base is a substance that removes hydrogen ions from a solution • Strong bases dissociate completely • Drain openers • Weak acids and bases do not dissociate completely • The body contains weak bases that are important in counteracting acids produced during cellular metabolism

19. Acids, Bases, and Salts (cont.) • Salts • An ionic compound consisting of any cation except a hydrogen ion and any ion except a hydroxide ion • They are held together by ionic bonds and dissociate easily in water • Salts are examples of electrolytes, inorganic compounds whose ions can conduct an electrical current in solution • Buffers and pH • Compounds that stabilize pH by either removing or replacing hydrogen ions • Antacids and baking soda

20. Carbohydrates • Carbs are organic molecules that contain carbon, hydrogen, and oxygen in a ratio near 1:2:1 • Includes sugars and starches which make up about half the typical US diet • Most important as sources of energy • Carbs are one of the 4 major classes of organic compounds • 3 major types of carbs: monosaccharides, disaccharides, and polysaccharides

21. Monosaccharides (simple sugars) • Carb containing from 3-7 carbon atoms • Includes glucose; the most important “fuel” for the body • Dissolve quickly and are rapidly distributed • Disaccharides • 2 monosaccharides joined together • Sucrose • Polysaccharides • Larger carb molecules that result when repeated dehydration synthesis reactions add additional monosaccharides or disaccharides • Starches and cellulose • Not easily broken down • Glycogen (animal starch) • A polysaccharide made of interconnected glucose • Stored in muscles as an energy reserve of glucose

23. Lipids • Contain a carbon-to-hydrogen ratio of 1:2 • Familiar lipids include fats, oils, and waxes • Most are insoluble in water, but special transport mechanisms carry them in the circulating blood • Provide about 2x as much energy as carbs when broken down in the body • The major types of lipids are fatty acids, fats, steroids, and phospholipids

25. Fatty Acids • Long chains of carbon atoms with attached hydrogen atoms that end in a carboxylic acid group (-COOH) • Only the carboxyl end dissolves in water • Saturated fatty acids have only single bonds between their carbons and unsaturated have 1+ double bonds • Fats • Fatty acids + glycerol = fat • Triglyceride = 3 fatty acids + glycerol • Energy reserves and insulation • Steroids • Large lipid molecules composed of four connected rings of carbon atoms • They differ in the carbon chains that are attached to the basic structure • Cholesterol is the best-known steroid • Phospholipids • Consists of a glycerol and 2 fatty acid linked to a nonlipid group by a phosphate group • The most abundant lipid components of cell membranes

26. Proteins • The most abundant organic components of the human body and in many ways the most important • Accounts for about 20% of the total body weight • Protein function • Support (structural proteins) • Create a 3D framework for the body • Movement (contractile proteins) • Responsible for muscle contraction • Transport • Transport proteins carry lipids, minerals, and gases through the blood • Buffering • Prevent dangerous changes in pH • Metabolic Regulation • Enzymes speed up chemical reactions in living things • Coordination and Control • Protein hormones can influence metabolic activities of every cells or affect the function of specific organs or organ systems • Defense • Waterproof proteins form the skin, hair, and nails and protect us from the environment. Antibodies protect us from disease. Clotting proteins restrict bleeding.

27. Protein Structure • Proteins are long chains of organic molecules called amino acids • There are 20 different amino acids that are the building blocks of proteins • Each amino acid consists of a central carbon atom bonded to a hydrogen atom, an amino group (-NH2), a carboxylic acid group (-COOH), and a variable R group or side chain • The name amino acid refers to the presence of an amino group and a carboxylic acid group • The amino acids are strung together like beads, with the carboxylic acid group of one attached to the amino group of another via a peptide bond • Peptides are molecules made up of amino acids held together by peptide bonds. • Polypeptides containing more than 100 amino acids are proteins • In a globular protein, like myoglobin, peptide chains fold back on themselves creating a rounded mass • The shape of a protein determines its function

28. Alanine (Ala) • Valine (Val) • Leucine (Leu) • Isoleucine (Ile) • Proline (Pro) • Methionine (Met) • Phenylalanine (Phe) • Tryptophan (Trp) • Glycine (Gly) • Serine (Ser) • Threonine (Thr) • Cysteine (Cys) • Asparagine (Asn) • Glutamine (Gln) • Tyrosine (Tyr) • Asparic Acid (Asp) • Glutamic Acid (Glu) • Lysine (Lys) • Arganine (Arg) • Histidine (His)

29. DNA and RNA • Nucleic acids are large organic molecules composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus • The 2 classes of nucleic acids are: • Deoxyribonucleic Acids (DNA) • Determines our inherited characteristics as well as all aspects of body structure and function • Ribonucleic Acids (RNA) • RNA cooperate to form specific proteins using the information provided by DNA

30. Structure of Nucleic Acids • Made up of subunits called nucleotides • Each nucleotide contains a sugar, a phosphate group, and a nitrogenous base • Sugar = 5 carbon (ribose or deoxyribose) • Nitrogenous bases = adenine, guanine, cytosine, thymine (DNA), or uracil (RNA)

31. ATP (Adenosine Triphosphate) • The energy that powers a cell is obtained by the breakdown of organic molecules • A high-energy bond is a covalent bond that stores an unusually large amount of energy • When the bond is later broken, the energy is later released under controlled conditions • In our cells, a high-energy bond usually connects a phosphate group to an organic molecule creating a high-energy compound • The most important is ATP • Made of AMP plus 2 phosphate groups or ADP plus 1 phosphate group • ADP to ATP is the primary method of energy storage, and the reverse reaction is the primary method of release • ADT + phosphate group + energy ATP + H2O

33. How to use a microscope

34. Introduction to the Microscope • Types • Care • Parts • Focusing

35. Types of Microscopes • Light Microscope • The models found in most schools, use compound lenses to magnify objects. The lenses bend or refract light to make the object beneath them appear closer. • Common magnifications: 40x, 100x, 400x • *Oil Immersion lenses can improve quality of focus and magnification

36. Types of Microscopes • Stereoscope • This microscope allows for binocular (two eyes) viewing of larger specimens. • Scanning Electron Microscope • Allow scientists to view a universe too small to be seen with a light microscope. SEMs do not use light waves; they use electrons (negatively charged electrical particles) to magnify objects up to two million times. • Transmission Electron Microscope • Also uses electrons, but instead of scanning the surface (as with SEM's) electrons are passed through very thin specimens.

37. Parts of a Microscope

38. Magnification • Your microscope has 3 magnifications: Scanning, Low and High. Each objective will have written the magnification. In addition to this, the ocular lens (eyepiece) has a magnification. The total magnification is the ocular x objective

39. General Procedures • 1. Make sure all backpacks and junk are out of the aisles. • 2. Plug your microscope in to the extension cords. Each row of desks uses the same cord. • 3. Store with cord wrapped around microscope and the scanning objective clicked into place. • 4. Carry by the base and arm with both hands.

40. Focusing Specimens • 1. Always start with the scanning objective. Odds are, you will be able to see something on this setting. Use the Coarse Knob to focus, image may be small at this magnification, but you won't be able to find it on the higher powers without this first step. Do not use stage clips, try moving the slide around until you find something. • 2. Once you've focused on Scanning, switch to Low Power. Use the Coarse Knob to refocus. Again, if you haven't focused on this level, you will not be able to move to the next level. • 3. Now switch to High Power. (If you have a thick slide, or a slide without a cover, do NOT use the high power objective). At this point, ONLY use the Fine Adjustment Knob to focus specimens. • 4. If the specimen is too light or too dark, try adjusting the diaphragm. • 5. If you see a line in your viewing field, try twisting the eyepiece, the line should move. That's because its a pointer, and is useful for pointing out things to your lab partner or teacher.

41. Drawing Specimens • 1. Use pencil - you can erase and shade areas • 2. All drawings should include clear and proper labels (and be large enough to view details). Drawings should be labeled with the specimen name and magnification. • 3. Labels should be written on the outside of the circle. The circle indicates the viewing field as seen through the eyepiece, specimens should be drawn to scale - ie..if your specimen takes up the whole viewing field, make sure your drawing reflects that. • Example:

42. Making a Wet Mount • 1. Gather a thin slice/piece of whatever your specimen is. If your specimen is too thick, then the cover slip will wobble on top of the sample like a see-saw, and you will not be able to view it under High Power. • 2. Place ONE drop of water directly over the specimen. If you put too much water, then the cover slip will float on top of the water, making it hard to draw the specimen, because they might actually float away. (Plus too much water is messy) • 3. Place the cover slip at a 45 degree angle (approximately) with one edge touching the water drop and then gently let go. Performed correctly the cover slip will perfectly fall over the specimen.

43. How to Stain a Slide • 1. Place one drop of stain (iodine, methylene blue..there are many kinds) on the edge of the cover slip. • 2. Place the flat edge of a piece of paper towel on the opposite side of the cover slip. The paper towel will draw the water out from under the cover slip, and the cohesion of water will draw the stain under the slide. • 3. As soon as the stain has covered the area containing the specimen, you are finished. The stain does not need to be under the entire cover slip. If the stain does not cover as needed, get a new piece of paper towel and add more stain until it does. • 4. Be sure to wipe off the excess stain with a paper towel.

44. Cleanup • 1. Store microscopes with the scanning objective in place.2. Wrap cords and cover microscopes.3. Wash slides in the sinks and dry them, placing them back in the slide boxes to be used later. 4. Throw cover slips away.

45. Troubleshooting • Occasionally you may have trouble with working your microscope. Here are some common problems and solutions. • 1. Image is too dark! • Adjust the diaphragm, make sure your light is on. • 2. There's a spot in my viewing field, even when I move the slide the spot stays in the same place! • Your lens is dirty. Use lens paper, and only lens paper to carefully clean the objective and ocular lens. The ocular lens can be removed to clean the inside. • 3. I can't see anything under high power! • Remember the steps, if you can't focus under scanning and then low power, you won't be able to focus anything under high power. • 4. Only half of my viewing field is lit, it looks like there's a half-moon in there! • You probably don't have your objective fully clicked into place.