Chapter 2 - Basic Chemistry notes PDF

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Just basic chemistry notes. Atoms and elements, types of bonds, and reactions and the types....

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BASIC CHEMISTRY Ch 2 – The Chemical Level of Organization (p. 28-39 in Tortora and Derrickson -15th Ed)

Why is it important to have a basic understanding of Chemistry before proceeding with the rest of the course? Studying anatomy involves learning about the structural make-up of our body parts - chemicals interacting with each other compose body parts. Studying physiology involves understanding the functions of our body parts - chemical reactions underlie physiological processes and determine body functions. The simplest level of structural organization in biology is the chemical level – atoms, molecules and macromolecules. • Chemistry - science of the structure and interactions of matter •

Matter - anything that occupies space and has mass - composes all living and non-living things - exists in 3 states: solid – definite volume and definite shape liquid – definite volume and takes shape of container gas – indefinite volume and indefinite shape What is mass? --- amount of matter composing an object; remains constant --- differs from the term “weight”; weight varies with the force of gravity (eg. you weigh almost nothing on the moon but your mass remains the same)

Atoms and Elements •

All matter is composed of chemical elements - elements cannot be chemically broken down into simpler substances by ordinary chemical means - are 118 recognized elements which are given a chemical symbol; symbol involves the letter(s) of element’s name or of its Latin or German name

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Are only 26 elements found in the human body most of our body mass (96%) is made up of only 4 major elements - carbon(C), hydrogen(H), nitrogen(N), and oxygen(O) - Ca, P, K, S, Na, Cl, Mg, Fe – comprise about 3.6% of total body mass (considered lesser elements) - Al, B, Cr, Co, Cu, F, I, Mn, Se, Zn and others occur in trace amounts (< 0.4% of body mass) Each element is composed of particles called atoms - “atom” is from a Greek word meaning “indivisible” and can be defined as the smallest unit of matter that retains the properties of its element - an atom is a cluster of even smaller subatomic particles which include: + 1. Protons - found in the nucleus (dense central core of the atom) and have a positive charge (p ) 0 2. Neutrons - found in the nucleus and have no charge (n ) -

3. Electrons - travel around the nucleus in orbitals (=shells) and have a negative charge (e ) - each shell holds a specific # of electrons - outermost shell is called the valence shell •

Atoms are electrically neutral # protons = # electrons (positive charge cancels the negative charge and total charge is zero)

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An atom of a certain element is defined by its: atomic number = # of protons mass number = # of protons + # of neutrons

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Protons and neutrons are heavy particles and have the same mass; electrons are tiny and have negligible mass in comparison mass of proton = 1 atomic mass unit (amu) mass of neutron = 1 amu mass of electron = 0 amu

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Isotopes are atoms of an element that vary in structure - an isotope of a certain element has the same # of protons but # of neutrons varies thus mass number will differ

Isotopes of the hydrogen atom. © Pearson Ed.2016 - nearly all elements have isotopes - most isotopes are stable, their nuclear structure does not vary over time - some are unstable with a nucleus that decays and emits radiation and are thus radioactive isotopes - radioactive isotopes can be used as “tracers” that are injected into the body to observe an organ’s function; a scanner is used to detect the emitted radiation to determine if function is normal What is carbon 14? --- it is a radioactive isotope that decomposes towards a more stable form --- the half-life of a radioisotope is the amount of time it takes for one-half (50%) of the atoms to decay (lose their activity) --- C14 has a long half-life of 5730 years and is used for dating archeological finds •

Scientists have organized the elements into the Periodic Table - are arranged from lowest to highest atomic number of the element horizontal rows 1  7 = periods - rows indicate the number of electron shells in each atom vertical columns I  VIII = groups - columns indicate the number of electrons in the outermost (valence) electron shell - elements in a column have the same physical and chemical properties information about any element can be found in the periodic table eg. oxygen atom

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Atomic mass (or weight) of an element is the average of the mass (atomic mass) of all its isotopes + 0 eg. You may expect the atomic mass to be 16 for oxygen since 8 p + 8 n = 16 amu, but it is 15.999. This value takes into account the weight of its isotopes and their abundance in nature (averages these).

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An atom becomes an ion (charged atom) when it gains or loses an electron (has a positive or negative charge) +2

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eg. Ca - calcium has 2 positive charges because it lost 2 electrons (has 20 p and 18 e ) + + Na - sodium lost 1 electron so has a positive charge (has 11 p and 10 e ) + Cl - chlorine has gained an electron so has a negative charge (has 17 p and 18 e )

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APPENDIX B – PERIODIC TABLE © John Wiley and Sons Inc. 2017

Structure of Atoms • Are two models of atomic structure:

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a) Orbital model (= electron cloud model) – depicts “probable” regions of greatest electron density by shading b) Planetary model (= electron shell model) – depicts electrons in circular orbitals or shells around the nucleus Planetary model is outdated, however it is still used (in your text) as it is easier to visualize the electrons in their shells

FIGURE 2.1, p. 30 - Two models depicting the atomic structure of the carbon atom. © John Wiley and Sons Inc. 2017

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Let’s look at some examples using the planetary model to depict atomic structure ---

** Try drawing out an atom of: (i.) potassium (K) given that it has an atomic # = 19 and a mass # = 39 and (ii.) iodine (I) given that it has an atomic # = 53 and a mass # = 127. (solution on p.8) Types of Chemical Bonds • Atoms do not exist in the free state but instead are combined with other atoms • A molecule is formed when 2 or more atoms of the same or different elements are joined by a chemical bond - can involve the same elements eg. H2, O2 - can involve different elements eg. CO2 What is a compound? --- it is a substance formed when different elements bind (eg. CO 2, CH4, H2O) thus all compounds are molecules but not all molecules are compounds •

A molecular formula indicates the type and number of each element making up a molecule eg. CO2 contains 1 atom of carbon and 2 atoms of oxygen

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Chemical bonds are formed to achieve complete valence shells of electrons and thus chemical stability - an atom with a completed valence shell is unreactive, that is it does not interact readily with other atoms - at the far right of the periodic table (column VIII) are helium, neon and argon which have full valence shells - these elements are said to be inert, meaning chemically unreactive - the reactivity of atoms arises from the presence of unpaired electrons in their valence shells - “Octet Rule” - atoms tend to interact so that each will have 8 valence electrons; an atom is chemically stable if the valence (outermost) shell has 8 electrons st

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- 1 shell has 2 e (shell nearest to the nucleus) nd - 2 shell has 8 e rd - 3 shell holds 8 or more e (maximum 18 e but is “satisfied” with 8) •

Bonds between atoms can be: 1. Ionic bonds - formed by the transfer of electrons from one atom to another eg. NaCl - recall, that atoms form ions when they gain or lose electrons - an atom that loses an electron is an electron donor and has a net positive charge (is a cation) - an atom that gains an electron is an electron acceptor and has a net negative charge (an anion) - oppositely charged ions attract and stay together to form an ionic bond

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FIGURE 2.4, p. 33 – Formation of an ionic bond. © John Wiley and Sons Inc. 2017 2. Covalent bonds - formed by the sharing of pairs of electrons between 2 or more atoms so each atom’s outer shell is filled (eg. CH4) and the electrons orbit around the molecule as a whole - most common type of bond in the body - covalent bonds can be – single -2 atoms share I pair of electrons - double -2 atoms share 2 pairs of electrons - triple -2 atoms share 3 pairs of electrons - sometimes 1 atom may attract the shared electrons more strongly than the other atom and the molecule is polar, creating a slightly more negative end while the other end of the molecule becomes slightly more positive - polar - e ’s not shared equally between atoms eg. H2O molecule is V-shaped - nonpolar - e ’s shared equally between atoms eg CO2 molecule is linear and symmetrical

FIGURE 2.5 (a-c), p.34 – Formation of covalent bonds involving sharing of 1, 2 or 3 pairs of electrons. © John Wiley and Sons Inc. 2017

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FIGURE 2.5 (d-e), p.34 – Formation of covalent bonds in which electrons are shared equally (d) and unequally (e) between two atoms. A water molecule has 2 poles of charge – a slightly more negative oxygen end δ and a slightly more positive + hydrogen end δ . Electrons are pulled more strongly to the oxygen end. © John Wiley and Sons Inc. 2017

3. Hydrogen bonds - formed when a hydrogen atom with a partial positive charge attracts the partial negative charge of a nearby electronegative atom (most often N or O) - form between different parts of large molecules such as DNA and proteins - are weak bonds

FIGURE 2.6, p. 35 – Hydrogen bonding among polar water molecules. Hydrogen atoms in one water molecule are attracted to the partial negative charge of the oxygen atom in another water molecule. © John Wiley and Sons Inc. 2017 Chemical Reactions •

Chemical reactions occur when bonds between atoms are formed, broken or rearranged

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A chemical equation is used to describe what happens in a reaction

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Total mass of the reactants = total mass of the products Number of atoms of each element stays the same

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Chemical reactions are reversible (occur in either direction) - however most biological reactions show little tendency to go in reverse It is the interactions of valence electrons that are the basis for all chemical reactions

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- atoms/molecules are in constant motion (more so in liquids and gases) and they need to collide forcefully to make or break chemical bonds - takes energy to start the reaction What is Energy? • •

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Energy is the capacity to do work There are two principle forms of energy: 1) Potential energy – energy stored by matter due to its position 2) Kinetic energy – energy associated with matter in motion Potential and kinetic energy takes on three forms in the body – chemical energy, electrical energy, and mechanical energy Chemical energy drives nearly all of our cellular processes and is stored in the chemical bonds of compounds and molecules

Types of Chemical Reactions • Chemical reactions occur when new bonds form or old bonds break between atoms •

Activation energy is the energy required to disrupt the electrons to get the molecules to interact - catalysts (enzymes) speed up reactions by lowering the activation energy

FIGURE 2.8, p. 37 – Activation energy is the energy needed to break chemical bonds in the reactant molecules so a reaction can start. © John Wiley and Sons Inc. 2017

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Chemical reactions are described as: 1. Synthesis reactions (anabolic process) - 2 or more atoms, ions, or small molecules together form a larger molecule; most are endergonic reactions (energy –using) eg.

A + B → AB 2H2 + O2 → 2H2O

2. Decomposition reactions (catabolic process) - a larger molecule is broken down into smaller molecules, ions or atoms; most are exergonic reactions (energy-releasing) eg. AB → A + B CH 4 → C + 2H2 3. Exchange reactions - involve both decomposition and synthesis eg.

- parts of 2 different molecules trade positions with one another AB + CD → AD + BC HCl + NaHCO3 → H2CO3 + NaCl

4. Oxidation-reduction reactions - decomposition reactions which produce ATP from food molecules - are also a type of exchange reaction as electrons are transferred between atoms and molecules - will be examined in more detail in Ch. 25

Examples of types of chemical reactions. © Pearson Ed.2016 What influences the speed of chemical reactions? •

An increase in temperature increases the kinetic energy of particles and increases the force of collisions between atoms/molecules as they move faster

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An increase in the concentration of reactants will increase the chance of successful collisions A decrease in particle size will increase molecular speed (particles move faster) and increase the reaction rate Presence of a catalyst (enzyme) lowers the energy needed to start the reaction so speeds up the process

**Solution – (i.) The nucleus of potassium contains 19 p+ and 20 no (39 -19 = 20 no). It is electrically neutral, so it would have 19 e-. Electron locations are: 2 in shell 1, 8 in shell 2, 8 in shell 3 and 1 in shell 4 (ii.) The nucleus of iodine contains 53 p+ and 74 no (127 – 53 = 74 no). It is electrically neutral, so it would have 53 e -. Electron locations are: 2 in shell 1, 8 in shell 2, 18 in shell 3, 18 in shell 4, and 7 in shell 5....