Anatomy & Physiology I Chemistry Pro: Manhal Chbat

How matter is organized  Chemical Elements: matter is composed of chemical elements, which can’t be broken down by ordinary chemical means.  Matter is anything that has mass and takes up space.  Matter can be found in three states; solid, liquid, gas.  Atoms: more-or-less identical building blocks for each element.  Atomic symbol is one-or-two-letter chemical shorthand.

Elements of the human body  Oxygen, carbon, hydrogen, nitrogen.  Lesser elements: make up 3.9 % of the body and include: Calcium (Ca), phosphorous (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium ( Mg), iodine (I), and iron (Fe).  Trace elements: makes up 0.01 % of the body. Required in minute amount and found as Co-enzymes.

Structure of the atom  The nucleus consists of neutrons and protons Neutrons– have no charge and a mass of one atomic mass unit (1 amu= dalton) Protons – positive charge and a mass of ( 1 amu= dalton)  Electrons are found orbiting the nucleus, have a negative charge with a very small mass to be considered ( 0 amu)

Atomic Number and Mass Number  Atomic number – equal to the number of protons  Mass number – is the sum of its protons and neutrons  Atomic weight – average of the mass numbers of all isotopes  Isotopes: are atoms with the same number of protons but a different number of neutrons.  Radioisotopes: are atoms that undergo spontaneous decay called radioactivity.

Ions, Molecules, & Compounds  Ions: atoms that gave up or gained electrons; symbol with (+)or (-).  Molecules: two or more atoms held together by chemical bonds.  Compound: two or more different kinds of atoms chemically bounded together (homogeneous) and cannot be separated physically.

Free Radicals  A free radical is an electrically charged atom or group of atoms with an unpaired electron.  Unstable and highly reactive; can become stable by giving up or gaining an electron (antioxidants are substances that inactivate oxygen-derived free radicals.)

Mixtures and Solutions  Mixture; tow or more components physically intermixed (not chemically bounded)  Solution; homogenous mixtures of components (solvent and solute)  Colloids (emulsion); heterogeneous mixture whose solutes do not settle out. (blood, milk, foam)  Suspensions; heterogeneous mixtures with visible solutes that tend to settle out. (flour or sand in water)

Chemical Bonds  Bonds are formed using the electrons in the outermost energy level.  Valence shell; outermost energy level containing active electrons.  Octet rule: except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their valence shell.  Inert element: outermost energy level fully occupied by electrons ( noble elements)

Types of Chemical Bonds  Ionic  Covalent  Hydrogen

Chemical Reactions  When chemical bonds are formed, rearranged, or broken.  How do we write a chemical reaction?  The total mass of reactants equals the total mass of the products.

Patterns of Chemical Reactions  Combination / synthesis reactions (anabolism): always involve bond formation; A + B  AB.  Decomposition reactions (catabolism): molecules are broken down into smaller molecules. AB  A + B  Exchange reactions: bonds are made and broken. AB + C  AC + B

Oxidation-Reduction (Redox) Reactions  Reactants losing electrons are electron donors and are oxidized.  Reactants taking up electrons are electron acceptors and become reduced.

Energy Flow in Chemical Reactions  Exergonic reactions: reactions that release energy (end products with less potential energy) / catabolism of food/.  Endergonic reactions: products contain more potential energy then did its reactants. (bonding amino acids to make proteins)

Reversibility of Chemical Reactions  All chemical reactions are theoretically reversible. A + B  AB AB  A + B  Equilibrium: when a chemical reaction proceeds in both directions at the same rate.

Factors Influencing the Rate of Reactions  Temperature  Partial size  Concentration  Catalysts  Enzymes

Energy  Energy is the capacity to do work.  Kinetic energy is the energy associated with matter motion.  Potential energy is energy stored by matter due to its position.

Biochemistry  Organic compounds: contain carbon and hydrogen, are covalently bonded, and are often large. examples??  Inorganic compounds: do not contain carbon and hydrogen. examples??

Water  Is the most important and abundant inorganic compound in all living systems.  Polar solvent properties:  High heat capacity:  Heat of vaporization:  Reactivity: hydrolysis and dehydration reactions  Cushioning: resilient cushion around certain body organs.

Salts, Acids, and Bases  Salts are inorganic compounds, contain cations other than H+ and anions other then OH-, are electrolytes and conduct electrical currents.  Acids release H+ and therefore proton donors HCl  (H+) + (OH-)  Bases release OH- and therefore are protons acceptors: NaOH  (Na+) + ( OH-)

Concept of pH  pH scale runs from 0 to 14 (concentration of H+ in moles/liter)  pH of 7 is neutral  (distilled water -- concentration of OH- and H+ are equal)  pH below 7 is acidic ([H + ] > [OH - ]).  pH above 7 is alkaline ([H + ] < [OH - ]).  pH is a logarithmic scale  Example: a change of two or three pH units  pH of 2 contains 10x10=100 more H+ than pH of 3  pH of 8 contains 10x10x10=1000 more H+ than pH of 11

Buffers Systems  Resist abrupt and large changes in the pH of the body fluids.  Usually consist of a weak acid and a weak base.  Carbonic acid-bicarbonate system: reversible releasing bicarbonate ions and protons.

Organic Compounds  Carbohydrates  Lipids  Proteins  Nucleic acids.

carbohydrates  Contain carbon, hydrogen, and oxygen  Provide most of the energy needed for life.  Three major groups:  Monosaccharides (glucose)  Disaccharides (sucrose)  Polysaccharides (glycogen)

Lipids  Like carbohydrates contain carbon, hydrogen, and oxygen; but less oxygen with fewer polar bonds which makes them hydrophobic  Mostly insoluble in polar solvent.  Combine with proteins (lipoprotein).  Major groups are: triglycerides, phospholipids, and steroid.

Triglycerides  Solid or liquid at the room temperature.  Energy, protection, and insulation functions.  Provide more than twice as much energy per gram as either proteins or carbohydrates.

Phospholipids and Steroids  Phospholipids: - Membrane components. - Amphipathic with both polar and nonpolar regions  Steroids: have four rings of carbon atoms and include: sex hormones, bile salt, some vitamins (vitamin D), adrenal cortical hormones and cholesterol.

Proteins  Constructed from 20 amino acids.  Dipeptides form combination of two amino acids joined by covalent bond called a peptide bond.  Polypeptides chains contain many amino acids joined by peptide bonds.  Both dipeptides and polypeptides are formed by dehydration synthesis.

Levels of Structural Organization  Includes: primary, secondary, tertiary, and quaternary.  Denaturation of protein means ………  Denaturation is usually caused by factors like ……..

Molecular Chaperones (Chaperonins)  Help other proteins to achieve their functional three- dimensional shape, folding integrity, translocation cross the membrane, and breakdown damaged protein.

Enzymes  Catalysts in living cells are called enzymes.  Highly specific in terms of the “substrate” with which they react.  Enzymes speed up chemical reaction by increasing frequency of collisions, lowering the activation energy and properly orienting the colliding molecules.  Their names usually end in –ase.

When reaction is complete, enzyme is unchanged and free to catalyze same reaction again on a new substrate Enzyme catalyzes reaction and transforms substrate into products Enzyme and substrate come together at active site of enzyme, forming an enzyme–substrate complex Glucose Fructose Enzyme Sucrase Active site of enzyme Substrates Sucrose and Water Products H2OH2O Mechanism of enzyme action 1 3 2

Nucleic Acids  Organic molecules that contain carbon, hydrogen, oxygen, nitrogen, and phosphorous.  The structural units are nucleotides, composed of a nitrogenous base, a pentose sugar, and a phosphate group.  The nitrogenous bases are: T, A, G, C, and U.  The major classes of nucleic acids are: DNA and RNA.

Deoxyribonucleic Acid (DNA)  Double-stranded helical molecule found in the nucleus.  Replicates itself before the cell divides, forms the genetic code inside each cell, and therefore regulating most of the cellular activities (instructions for protein synthesis, genetic continuity) throughout lifetime.

Ribonucleic Acid (RNA)  Single-stranded molecule found in the nucleus and the cytoplasm.  Relays instructions from the DNA to guide each cell’s assembly of amino acids into proteins by the ribosome.  Differs from the DNA: single stranded, ribose sugar, uracil replaces thymine.  Major types: messenger, ribosomal, and transfer

Adenosine Triphosphate (ATP)  Source of immediately usable energy for the cell  Adenine-containing RNA nucleotide with three phosphate groups.  Hydrolysis of ATP: removal of phosphate group by enzyme – ATP ase which releases energy and leave ADP.  Synthesis of ATP: addition of the terminal phosphate group by ATP synthase to ADP which requires the use of energy that comes from the glucose molecules. ( aerobic and anaerobic respiration)