Chapter 2 Basic Chemistry - Chemistry Text PDF

Chapter 2 Matter Basic Chemistry Chemicals take up space and have mass Exists as elements (pure form) and in chemical combinations called compounds 1  Elements can’t be broken down into simpler substances by chemical reaction and are composed of atoms Ele...

Chapter 2 Matter Basic Chemistry Chemicals take up space and have mass Exists as elements (pure form) and in chemical combinations called compounds 1  Elements can’t be broken down into simpler substances by chemical reaction and are composed of atoms Elements Essential elements in living things include carbon C, hydrogen H, oxygen O, and nitrogen N making up 96% of an organism A few other elements Make up the remaining 4% of living matter H C N O Na Mg P S K Ca 2  If there is a deficiency of an essential element, disease results Figure 2.3 (b) Iodine deficiency (a) Nitrogen deficiency (Goiter) Trace elements are required by an organism in only minute quantities Minerals such as Fe and Zn are trace elements 3  Compounds are substances consisting of two Compounds or more elements combined in a fixed ratio Have characteristics different from those of their elements + Figure 2.2 Sodium Chloride Sodium Chloride 4  An element’s properties depend on the structure of its atoms Properties of Matter Each element consists of a certain kind of atom that is different from those of other elements An atom is the smallest unit of matter that still retains the properties of an element Atoms of each element are composed of even smaller parts called subatomic particles Neutrons- no electrical charge Protons- positively charged Electrons-negatively charged 5  Protons and neutrons – Are found in theParticle Subatomic atomic Location nucleus Electrons – Surround the nucleus in a “cloud” Cloud of negative Electrons charge (2 electrons) Nucleus Figure 2.4 (a) This model represents the electrons In this even more simplified model, the as a cloud of negative charge, as if we (b) electrons are shown as two small blue had taken many snapshots of the 2 spheres on a circle around the nucleus. electrons over time, with each dot 6 representing an electron‘s position at one point in time.  Atoms of the various elements Differ in their number of subatomic particles Atomic Number & Atomic Mass The number of protons in the nucleus = atomic number ○ The number is protons determines what the element is The atomic number is unique to each element and is used to arrange atoms on the Periodic table Carbon = 12 Oxygen = 16 Hydrogen = 1 Nitrogen = 17 7 Atomic Mass Is an approximation of the atomic mass of an atom It is the average of the mass of all isotopes of that particular element decimal number Protons and neutrons do not have to be the same number Example: Carbon(atomic number 6) has 3 naturally occurring forms- one with 6 neutrons, one with neutrons, one with 8 8 neutrons Mass Number The number of protons + neutrons = atomic mass Can be used to find the number of neutrons (Subtract atomic number from atomic mass) 9  The Most Common Biological Atoms Carbon- Can make 4 covalent bonds. Hydrogen- Can only make 1 covalent bond. Phosphorus- Can make 5 covalent bonds. Oxygen- Can make 2 covalent bonds. Nitrogen- Can make 3 covalent bonds. Isotopes Different forms of the same element Have the same number of protons, but different number of neutrons May be radioactive spontaneously giving off particles and energy May be used to date fossils or as medical tracers 11 APPLICATION Scientists use radioactive isotopes to label certain chemical substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA. Ingredients including Radioactive tracer Incubators (bright blue) 1 2 3 TECHNIQUE 10°C 15°C 20°C Human cells 4 5 6 25°C 30°C 35°C 1 Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a 7 8 9 40°C 45°C 50°C radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H. DNA (old and new) 2 The cells are placed in test tubes, their DNA is isolated, and unused 1 2 3 4 5 6 7 8 9 ingredients are removed. 12 3 A solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter. RESULTS The frequency of flashes, which is recorded as counts per minute, is proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C. Optimum 30 temperature Counts per minute for DNA synthesis (x 1,000) 20 10 0 10 20 30 40 50 Figure 2.5 Temperature (°C) 13  An atom’s electrons Vary in the amount of energy they possess Energy Levels Electrons further ofnucleus from the Electrons have more energy Electron’s can absorb energy and become “excited” Excited electrons gain energy and move to higher energy levels or lose energy and move to lower levels 14  Energy – Is defined as Electrons and Energythe capacity to cause change Potential energy - Is the energy that matter possesses because of its location or structure Kinetic Energy - Is the energy of motion The electrons of an atom – Differ in the amounts of potential energy they possess (a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can only rest on each step, not between 15 Figure 2.7A steps. Energy Levels Are represented by electron shells Third energy level (shell) Second energy level (shell) Energy absorbed First energy level (shell) Energy lost Atomic nucleus (b) An electron can move from one level to another only if the energy it gains or loses is exactly equal to the difference in energy between the two levels. Arrows indicate some of the step-wise changes in Figure 2.7B potential energy that are possible. 16  Electron Configuration and Chemical Properties The chemical behavior of an atom – Is defined by its electron configuration and distribution Why do some elements react? Valence electrons – Are those in the outermost, or valence shell – Determine the chemical behavior of an atom Atoms tend to -complete a partially filled valence shell or -empty a partially filled valence shell 17 This tendency drives chemical reactions…  Chemical Bonding Hydrogen atoms (2 H) Covalent Bonds In each hydrogen 1 atom, the single electron Sharing of a pair of valence is held in its orbital by its attraction to the + electrons + proton in the nucleus. Examples: H2 When two hydrogen 2 atoms approach each Molecule- Consists of two or other, the electron of each atom is also more atoms held together by attracted to the proton + + in the other nucleus. covalent bonds Single bond- the sharing of one The two electrons 3 become shared in a pair of valence electrons covalent bond, forming an H2 molecule. + + Double bond- the sharing of two Hydrogen Figure 2.10 molecule pairs of valence electrons (H2) 18 Two Main Types of Covalent Bonds Non- Polar Covalent Bonds- Atoms share electrons equally, formed between atoms with identical electronegativity. Polar Covalent Bonds- Atoms with different electronegativities do not share electrons equally, one atom has a more negative charge, the other more positive. ○ One atom has a slightly greater pull on the shared electrons. ○ Polarity- Separation of charge into distinct positive and negative regions. ○ Ex. Water, Ions  Electronegativity – Is the attraction of a particular kind of atom for the Covalent Bonding electrons in a covalent bond The more electronegative an atom – The more strongly it pulls shared electrons toward itself In a nonpolar covalent bond – The atoms have similar electronegativities – Share the electron equally Name Structural Space- filling Electron-shell (molecular formula) formula model diagram Oxygen (O2). Two oxygen atoms share two pairs of O O Figure 2.11 B 20 electrons to form a double bond.  Covalent Bonding cont. In a polar covalent bond – The atoms have differing electronegativities – Share the electrons unequally Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. δ– This results in a partial negative charge on the oxygen and a partial positive O charge on the hydrogens. Figure 2.12 H H δ+ δ+ H2O 21 Polarity General Rule of Thumb for Non-polar Molecules: ○ Hydrocarbons are generally non polar (hydrocarbons are basically carbons surrounded by hydrogens, ex. Lipids). ○ Hydrocarbons tend to be in long chains or rings. ○ Very little O and N atoms present (if at all). General Rule of Thumb for Polar Molecules: ○ Contains a higher ratio of O, or N atoms. (These are the most common in biological molecules you will see in this course). ○ (More electronegative, more likely to form polar covalent bonds). Ionic Bonds In some cases, atoms strip electrons away from their bonding partners Electron transfer between two atoms creates ions Ions – Are atoms with more or fewer electrons than usual – Are charged atoms An anion – Is negatively charged ions A cation – Is positively charged 24  An ionic bond – Is an attraction between anions and cations 2 1 The lone valence electron of a sodium Each resulting ion has a completed atom is transferred to join the 7 valence valence shell. An ionic bond can form electrons of a chlorine atom. between the oppositely charged ions. + – Na Cl Na Cl Na+ Cl– Na Cl Sodium ion Chloride ion Sodium atom Chlorine atom (a cation) (an anion) Figure 2.13 (an uncharged (an uncharged atom) atom) Sodium chloride (NaCl) Ionic compounds – Are often called salts, which may form crystals 25 Weak Chemical Bonds Several types of weak chemical bonds are important in living systems Reinforce the shapes of large molecules Help molecules adhere to each other Hydrogen Bonds A hydrogen bond – Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen 26 atom of ammonia. Van der Waals interactions – Occur when transiently positive and negative regions of molecules attract each other – This is an interaction between different molecules without any chemical bonds being made/broken- very weak and short lived We will talk about these and their significance next chapter  Molecular shape Shape and Function – Determines how biological molecules recognize and respond to one another with specificity Structure determines Function! The precise shape of a molecule – Is usually very important to its function in the living cell – Is determined by the positions of its atoms’ valence orbitals Three p Four hybrid orbitals Z orbitals In a covalent bond s orbital – The s and p orbitals may X hybridize, creating specific Y molecular shapes Tetrahedron  Carbon Nitrogen Hydrogen Sulfur Oxygen Natural endorphin Morphine (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. Natural endorphin Morphine Brain Endorphin cell receptors (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Figure 2.17 29  A Chemical reaction – Is the making and breaking of chemical bonds – Leads to changes in the composition of matter Chemical reactions – Convert reactants to products + 2 H2 + O2 2 H 2O Reactants Reaction Product Chemical equilibrium – Is reached when the forward and reverse reaction rates are equal 30