Biol 109[topic_1]2021-1.docx

**Biol 109 R. JUSTIN TAYLOR** **Topics 1** **[Chemistry of Living Organisms]** **A. Matter** **[GENERAL CHARACTERISTICS]** Matter may be defined as anything that has mass and occupies space (has volume) and resists a change in motion Matter is made of small [particles](http://simple.wikipedia....

**Biol 109 R. JUSTIN TAYLOR** **Topics 1** **[Chemistry of Living Organisms]** **A. Matter** **[GENERAL CHARACTERISTICS]** Matter may be defined as anything that has mass and occupies space (has volume) and resists a change in motion Matter is made of small [particles](http://simple.wikipedia.org/wiki/Particle), too small for the eye to see. Most common matter is made of particles called [atoms](http://simple.wikipedia.org/wiki/Atom). Atoms are made of even smaller particles called [subatomic particles](http://simple.wikipedia.org/wiki/Subatomic_particle). **ATOMS** An atom is the smallest part of an element that retains the chemical properties of that particular element, for e.g., hydrogen (h) is an atom; oxygen (O) is an atom and so on. The atom is comprised of smaller particles known as subatomic particles, i.e., protons, neutrons and electrons. The particle composition, i.e., the amount of protons, neutrons and electrons present reflects the differences in each atom. This is how one is able to differentiate H from O or N or Mg, etc. Matter comes predominantly in 3 forms: 1. **solids** -- can change their size and shape; e.g., wood, blackboard, floor, desk 2. **Liquids** -- has no definite shape: takes on the shape of its container; has volume; can flow, be poured or spilled to take the shape of the surface it is on. 3. **Gases** -- has no shape or volume; takes on the shape of its container; can be felt as wind; it is invisible and sometimes odorless. Melting boiling freezing condensation **[ELEMENTS]** -- Obtain a print out of the periodic table An element is what makes up matter like how many bricks make a house or how amino acids make up proteins or how simple sugars make up starch. Elements are essentially the building blocks of matter. Also, an element is classified as Matter that cannot be broken down into simpler substances by chemical reactions is known as There are about 109 elements (sources differ). The most important include the metals, non-metals and metalloids. The elements are in turn comprised of atoms. Four most common elements found in living organism's carbon, oxygen, nitrogen, and hydrogen - Carbon (C) is most important in the human skeletal structure; All living organisms contain **carbon**; the human body is about 18% **carbon** by weight. - Oxygen (O) is absolutely vital for sustaining life as we know it and of the five basic elements of all life on earth, **oxygen** is the most abundant; as a component of water, it is also important in body water health - Hydrogen (H) forms bonds with most elements therefore is an important molecular and structural constituent - Nitrogen (N) is unique to proteins and is a primary component in the structure of proteins and nucleic acids. - Sulfur (S) is a major component of essential amino acids that make up protein that the body needs - Phosphorus (P) is important in the blood buffering system Trace elements are also important in the functioning of the human body. - Trace elements can be defined as elements required in minute amounts to maintain a healthy body; needed mainly as components of enzymes and hormones, or are involved in the activation of enzymes. - [F](http://www.answers.com/topic/fluorine)luoride (used in toothpaste to aid in healthy teeth and gums); - [Chromium](http://www.answers.com/topic/chromium) (enhances the action of insulin, a hormone critical to the metabolism and storage of carbohydrate, fat, and protein in the body); - [Cobalt](http://www.answers.com/topic/cobalt) (a central component of the [vitamin](http://en.wikipedia.org/wiki/Vitamin) [cobalamin](http://en.wikipedia.org/wiki/Cobalamin), or [vitamin B~12~](http://en.wikipedia.org/wiki/Cyanocobalamin)); - Copper, [iodine](http://www.answers.com/topic/iodine), [manganese](http://www.answers.com/topic/manganese), and [selenium](http://www.answers.com/topic/selenium) are other important trace elements.   Water considered a polar molecule because the oxygen end of the molecule has a slight negative charge, and the hydrogen end has a slight positive charge. **[ATOMIC STRUCTURE]** ***Bohr Model (1915)*** The Bohr model depicts the structure of an atom where electrons are configured in a series of concentric rings (circles) around the atom's nucleus. The nucleus or center is comprised of the protons and neutrons. Isotopes of an element have the same number of protons and different numbers of neutrons. 1. **Protons (p)** -- massive particles with a **positive electric charge**; it is used to identify an atom by its number. Look at the periodic table; each element has a number above its symbol called the atomic number which is also known as the proton number. So if you know the atomic number then the proton number is the same and vice versa. For e.g., H is the symbol for hydrogen which has an atomic number of 1, therefore 1 is also its proton number. 2. **neutrons** **(n)** -- has no electrical charge 3. **Electrons (e-)** -- has a negative electric charge with very little mass; no fixed location because it moves very rapidly; It is not in the nucleus but instead circles the nucleus. - Protons and neutrons are found in the nucleus. Electrons occupy a large region of space around the nucleus (electron cloud) and are in motion. - [Atomic number]: number of protons. Each element has a different atomic number. - Elements in the periodic table are listed according to increasing atomic number. - [Mass number]: total number of protons and neutrons in nucleus of an atom - [Average atomic mass]: weighted average of the masses of all the different isotopes of an element Use the following to determine the amount of each subatomic particle in an atom: For any element: Number of Protons = Atomic Number Number of Electrons = Number of Protons = Atomic Number Number of Neutrons = Mass Number (atomic weight) - Atomic Number View your periodic table you printed out and determine if the following is true for krypton: Number of Protons = Atomic Number = 36 Number of Electrons = Number of Protons = Atomic Number = 36 Number of Neutrons = Mass Number - Atomic Number = 84 - 36 = 48 - **Let's take a look at the atom structure.** **[BONDING OR *Chemical Bonding*]** This refers to the force that holds two atoms together in a compound where an atom's valence (outermost) electrons join to form a molecule, compound or larger structure like a crystal. ***Types of bonding:*** 1. ***covalent*** -- strongest of the bonds; involves the sharing of electrons between 2 or more atoms; it is more common than ionic bonds; covalent bonds result in the formation of 'true' molecules unlike with ionic bonds which form ions; the covalent bond tends to move about freely and **exist as liquids or gases** at Rm. Temp.; e.g., two H atoms join to form H~2~; A single covalent bond is formed; In the case of multiple bonds, i.e., double or triple bonds, Oxygen and Nitrogen are good examples: 2. ***ionic*** -- a weak bond like that of the hydrogen bond; **Ionic bonds are characterized by Atoms giving away and taking electrons** **[COMPOUNDS]** A compound is a substance formed when two or more elements are chemically joined. Water, salt, and sugar are examples of compounds. When the elements are joined, the atoms lose their individual properties and have different properties from the elements they are composed of. A chemical formula is used a quick way to show the composition of compounds. Letters, numbers, and symbols are used to represent elements and the number of elements in each compound. They usually have a fixed ratio, for e.g., water (H~2~O) which is also known as **di**hydrogen **mono**xide; Magnesium nitrate or MgNO^3-^; Ammonia or NH~3~, Methane or CH~4~. Compounds function differently than the elements that comprise them, e.g., Fe-iron (metal) and O-oxygen (odorless gas) form FeO or rust that functions quite differently than Fe or O alone. **[BUFFERS]** These are chemicals (ionic compounds) containing both an acid and base that resists changes in its pH. Buffers function to maintain a specific pH range above or below neutral or whatever specific pH range needs to be maintained; some examples of buffers or buffer systems are - Proteins - different pH\'s will cause molecules to gain and loose electrons and protons (ionize). If proteins are not kept at the proper pH they will not function properly; pH is probably the most important single thing the body regulates since it will affect so many other processes. - Sodium bicarbonate buffers in the blood - Phosphate buffers in the blood - CaCO~3~ (baking soda) - Carbonic acid- bicarbonate buffer system in the blood that basically equalizes the pH of your blood - Eye drops used to create a chemical balance in the eye acts as a buffer - Insulin acts as a buffer to maintain proper blood glucose levels **B. Organic Compounds in protoplasm** **[­PROTOPLASM]** This refers to the fluid constituent of the cell which is comprised of the cytoplasm and nucleoplasm; also referred to as the living substance of the cell. Within the protoplasm are a number of cell components and substances, however, we will only highlight the following: 1. carbohydrates 2. lipids 3. proteins 4. nucleic acids Polymers are formed by joining of monomers by Condensation **[Carbohydrates:]** Obtain a 6-C glucose structure - - - - - - - - - - - - - **[Lipids]** Obtain the structure of a lipid showing the fatty acid and glycerol molecule to which they are attached. - Insoluble in water; soluble in organic solvents like ether or chloroform - Its basic structure includes fatty acids attached to a glycerol molecule - Lipids are grouped as fat which is a solid at Rm. Temp. or oils which is a liquid at Rm. Temp. - Are divided into simple and complex fats - Lipids are also characterized as saturated (animal source) or unsaturated (veggie source) - Excessive consumption of animal fats (saturated) are a health risk that cause high cholesterol and ultimately, vascular disease - Lipids provide more energy than carbs or proteins, i.e., 9cal/g; it is a concentrated energy source - Used as an energy source, as a component of cell membranes, and to make compounds - 3 polyunsaturated f.a. (C-18:1/2/3) are essential and with non-lipid nutrients makes all the lipid compounds the body requires - Animal foods - rich in saturated fats and cholesterol (egg yolks, butter and meat) - Plant foods -- most contain unsaturated fats, i.e. corn, soy, cottonseed, safflower, olive, canola, and peanut oils; - Palm and coconut oils are high in saturated fats, including butter - Important part of the cell structure - Transports vitamins A, D, E and K **[Protein]** Glycine is the simplest amino acid. Obtain a diagramme of glycine. - Are comprised of 20 amino acids; some (\~8) are essential -- must be obtained as an external source - Basic amino acid structure is comprised of: an amine group, ketone group and an 'R' group - The shape of protein dictates its function - Proteins are polymers constructed from amino acids monomers - provides 4cal/g of energy - Function as enzymes \[all enzymes are proteins but not all proteins are enzymes; egg albumin (egg white) is a protein but it is not an enzyme\] - Used to make substances such as hemoglobin (blood protein) and myosin (muscle protein) - Source of complete protein foods include eggs, milk, meat and fish - Excess amino acids in the blood is taken up by the liver, deaminated to form NH~3~ that is converted to urea and excreted; the remaining C-chain (keto acid) is converted to carbs or lipids and used for energy or stored - Major component of body tissue needed for its growth and repair **[Nucleic acids]** - Consists of DNA (contains genetic material) and RNA, nutrient supplements - DNA is made of units called nucleotides which consist of a base, sugar and phosphate group - Only essential in conditions of rapid growth, limited food supply and metabolic stress - monomer is used to build RNA and DNA called nucleotide **[The Cell in Structure and Function]** **A. Structure** **[Cell Membrane]** - Surrounds each cell organelle - The membrane controls what goes in and out of the cell; - Proteins in the bilayer deal with communication and regulate the movement of water and soluble molecules through the membrane. - Transport is either active or passive. - ***Active*** transport is moving molecules against the concentration gradient and energy is required in the form of ATP. - ***Passive*** transport is moving molecules down the concentration gradient and no energy is required. E.g., **diffusion**, which moves from high concentration to low concentration and **osmosis**, which is the diffusion of water molecules. - The cell membrane is important for the connections between cells. **[Nucleus]** - Surrounded by a nuclear membrane that is 2 layers thick; contains openings called nucleopores for transport in and out of the nucleus; spherical in shape; 1 or more per cell; Contains chromosomes which contain the genetic information (DNA); spherical nucleolus within which contain RNA that synthesize (makes) protein. **Information is transferred from the nucleus to ribosomes via mRNA. communicates with the surrounding cytosol via numerous *nuclear pores*.** **[Mitochondria]** **[Major differences between plant and animal cells]** **Property** **Plant Cells** **Animal Cells** --------------------- ----------------- ------------------ Cell Wall Present Absent Chloroplasts Present Absent Lg. Central Vacuole Present Absent Lysosomes Absent Present Cell shape - If a cell\'s lysosomes burst, the cell would digest itself - Protists, Fungi, Plants, Animals all belong to what group of cells Eukaryotes - The extracellular matrix of animal cells protects and supports cells - Cellular respiration can be described as the conversion of the energy stored in food molecules to energy stored in ATP **Nucleolus** - **\*ER** - - - - **\*Golgi apparatus** - - - **Cell membrane** - - - **Cell wall** - - - **Cytosol (cell substance)** - **Mitochondrion** - - **Chloroplasts** - - - **Vacuoles** - - **Centrosome** - - **Cytoskeleton** - - B. **Function of the membrane in transport of substances in and out of the cell** **[Diffusion]** - Diffusion is the net movement of molecules (ions or particles) from a region of high concentration to a region of lower concentration due to random motion of molecules or the movement of molecules and ions down their concentration gradient - proceeds until a dynamic equilibrium is reached - Heating the solution can speed up diffusion in a solution. This makes sense when you consider that heat is the total amount of kinetic energy in a solution. Likewise to slow diffusion down the solution can be cooled. - Because diffusion requires kinetic energy from the environment but does not require cellular energy (from the cell) it is a form of **passive transport**. - E.g., the movement of perfume in the classroom; a spray of air freshener in a room; a drop of dye in a beaker of water; - Diffusion may also occur across a membrane but it must be permeable (allows fluide to penetrate or pass through) - Diffusion stops when the concentration on either side of a membrane is equalized. **[Osmosis]** - Special case of diffusion where water moves from a high to low water concentration across a semi-permeable (allow certain molecules to pass through) membrane **Osmosis,** like **diffusion** in general does not require any cellular energy but just the kinetic energy related to the heat on either side of the membrane When two solutions that differ in solute concentration are placed on either side of a selectively permeable membrane, and osmosis is allowed to take place, the water will, exhibit a net movement to the side with lower water concentration