•Matter consists of chemical elements in pure form and incombinations called compounds•Organisms are composed of matter, which is anythingthat takes up space and has mass •Mass is the amount of matter in an object •Weight is a measure of how strongly that mass is pulled by gravity•Matter is made up of elements, substances that cannotbe broken down to other substances by chemicalreactions•A compound is a substance consisting of two or moreelements combined in a fixed ratio and hascharacteristics different from those of its elements
A compound Is a substance consisting of two or more elements combined in a fixed ratio Has characteristics different from those of its elements + Sodium Chloride Sodium Chloride
Essential elements Include carbon, hydrogen, oxygen , and nitrogen Make up 96% of living matterA few other elements Make up the remaining 4% of living matter
The effects of essential element deficiencies (a) Nitrogen deficiency (b) Iodine deficiency Controlled experiment Enlarged Thyroid gland – iodine is a trace element
Each element Consists of a certain kind of atom that is different from those of other elementsAn atom Is the smallest unit of matter that still retains the properties of an elementAtoms of each element Are composed of even smaller parts called subatomic particles
Simplified models of an atom Neutrons, which have no electrical Cloud of negative Electrons charge charge (2 electrons) Protons, which are Nucleus positively charged Electrons, which are negatively charged (a) (b) In this even more simplified This model represents the electrons as a cloud of model, the electrons are negative charge, as if we had shown as two small blue taken many snapshots of the 2 spheres on a circle around the electrons over time, with each nucleus. dot representing an electron‘s position at one point in time.
The atomic number of an element Is the number of protons Is unique to each element Carbon has 6 protons, any atom with 6 protons is carbon The mass number of an element Is the sum of protons plus neutrons in the nucleus of an atom Carbon can exist with 6, 7, or 8 neutrons – 12C, 13C, or 14C These are isotopes of carbon Is an approximation of the atomic mass of an atom
Isotopes of a given element Differ in the number of neutrons in the atomic nucleus Have the same number of protons Radioactive isotopes Spontaneously give off particles and energy
Can be used in biology 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. TECHNIQUE Ingredients including Radioactive tracer Incubators (bright blue)Proliferation assay 10°C 1 2 15°C 3 20°C Human cells Ingredients for 4 5 6 25°C 30°C 35°C 1 making DNA are added to human cells. One 7 8 9 ingredient is labeled with 3H, a 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. The cells are placed in test 2 tubes, their DNA is isolated, DNA (old and new) and unused ingredients are removed. 1 2 3 4 5 6 7 8 9
A solution called scintillation fluid is added to the test tubes 3 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 RESULTS clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C. Optimum Counts per minute 30 temperature for DNA (x 1,000) 20 synthesis 10 0 10 20 30 40 50Figure 2.5 Temperature (°C)
Glucose labeled with a radioactive isotope is injected into the patient Chemically active areas can be seen on this PET scan Cancerous throat tissue
Energy Is defined as the capacity to cause change Potential energy Is the energy that matter possesses because of its location or structure The electrons of an atom Differ in the amounts of potential energy they possess – because of their position
Rows represent a new valence shell of electrons Valence shells have to be full before going to the next level Maximum amount in valence shells: 2, 8, 8, 18, 18, 32 Electrons like to be paired Groups S, D, P, and F Potassium: 1s12s22p63s23p64s1 Energy Tree Spin rotation “Latice Energy”
Columns represent similar chemical characteristics Similar properties Similar chemical properties, melting point, boiling point, freezing point, (ability to rust) oxidation etc. Copper, Silver, and gold are all in the same column What do they have in common?
Energy levels Are represented by electron shells These Third energy level (shell) electrons are more likely to Second energy level (shell) _ Energy _ “do absorbed something” _ First energy level (shell) Energy + lost Atomic nucleus
The chemical behavior of an atom – what it does Is due to its electron configuration and distribution The periodic table of the elements Shows the electron distribution for all the elements Hydrogen 2 Atomic number Helium He 2He 1H 4.00 Element symbol Atomic mass First Electron-shell shell diagram Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon 3Li 4Be 3B 6C 7N 8O 9F 10Ne Second shell Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon 11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar Third shellFigure 2.8
Valence electrons 1. Are those in the outermost, or valence shell 2. Determine the chemical behavior of an atom
Are the three-dimensional space where an electron is found 90% of the time Each electron shell Consists of a specific number of orbitals Electron orbitals. Each orbital holds up to two electrons. x Y Z 1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. (a) First shell (b) Second shell (c) Neon, with two filled shells (maximum (maximum (10 electrons) 2 electrons) 8 electrons)
A covalent bond Is the sharing of a pair of valence electrons
Formation of a covalent bond Hydrogen atoms (2 H) 1 In each hydrogen atom, the single electron is held in its orbital by + + its attraction to the proton in the nucleus. 2 When two hydrogen atoms approach each other, the electron of each atom is also + + attracted to the proton in the other nucleus. 3 The two electrons become shared in a covalent bond, + + forming an H2 molecule. Hydrogen molecule (H2)Figure 2.10
A molecule Consists of two or more atoms held together by covalent bonds A single bond Is the sharing of one pair of valence electrons A double bond Is the sharing of two pairs of valence electrons
Name Electron- Structural Space- (molecular shell formula filling formula) diagram model (a) Hydrogen (H2). Two hydrogen H H atoms can form a single bond. (b) Oxygen (O2). Two oxygen atoms share two pairs of O O electrons to form a double bond.Figure 2.11 A, B
Covalent bonding in compounds Name Electron- Structural Space- (molecular shell formula filling formula) diagram model (c) Water (H2O). Two hydrogen atoms and one O H oxygen atom are joined by covalent H bonds to produce a molecule of water. (d) Methane (CH4). Four hydrogen atoms can satisfy H the valence of one carbon atom, forming H C H methane. HFigure 2.11 C, D
Electronegativity Is the attraction of a particular kind of atom for the 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 – carbon/hydrogen
In a polar covalent bond The atoms have differing electronegativities Share the electrons unequally Oxygen, nitrogen, and phosphorous Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. have large nuclei – which attract the electrons strongly. This results in a partial negative charge on the oxygen and a partial positive O charge on the hydrogens.Figure 2.12 H H + + H2O
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
An ionic bond Is an attraction between anions and cations 1 The lone valence electron of a sodium 2 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– Sodium on Chloride ion Na Cl (an anion) Chlorine atom (a cation) Sodium atom (an uncharged (an unchargedFigure 2.13 atom) atom) Sodium chloride (NaCl)In water (our bodies) these ionic bonds do not hold so we have ions (very important to cells)
Ionic compounds Are often called salts, which may form crystals Not called molecules Na+ Cl–Figure 2.14
Several types of weak chemical bonds are important in living systems (in aqueous environments) Ionic bonds Hydrogen bonds Van der Waals interactions Occur when transiently positive and negative regions of molecules attract each other only when they are very close Hydrophobic interactions
A hydrogen bond Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom – +Notice water Water His polar! (H2O) O A hydrogen bond results These molecules H from the attraction are hydrophilicRemember between the water-loving + partial positivecells are in an – charge on theaqueous hydrogen atom of water and So are ions. Ammonia the partialenvironment. (NH3) N negative charge on the nitrogen H H atom of + H + ammonia. Figure 2.15 +
Sharing in covalent bond formation can be unequal (polar). Large atomslike oxygen or nitrogen have large nuclei with powerful positive charges.These nuclei tend to pull the electrons so that they spend more timearound the large nuclei (O), leaving the molecule with a partial negativecharge in that area and a partially positive chargearound the smaller nuclei (H).These molecules are polar.The weak attraction betweenthese partial charges is calleda hydrogen bond.Water is a polar compoundand many of it’s importantqualities is due to it’s polarityand it’s ability to form hydrogen bonds between water moleculesand between water and other molecules and ions.
Several types of weak chemical bonds are important in living systems (in aqueous environments) Ionic bonds Hydrogen bonds Van der Waals interactions Occur when transiently positive and negative regions of molecules attract each other only when they are very close – more to do with fit. Hydrophobic interactions
Hydrophobic interactionsThe polypeptidebackbone is hydrophilic waterbut the hydrogen bondskeep the backboneinternal,with hydrophobic amino hydrophobicacids facing out –interacting with the fattyacids of the membrane. water
Weak chemical bonds Determine and reinforce the shapes of large molecules Help molecules adhere to each other The precise shape of a molecule Is very important to its function in the living cell Is determined by the positions of its atoms’ valence orbitals
This gives each molecule,no matter how small orlarge, a specific shape anda characteristic chemicalnature. Space-filling Ball-and-stick Hybrid-orbital model model model (with ball-and-stick Unbonded model superimposed) Electron pair O O H H H H Water (H2O) 104.5° H H C C H H H H Methane (CH4) H H
Carbon Nitrogen Hydrogen SulfurMolecular shape Oxygen Naturaldetermines how endorphin Morphinebiological moleculesrecognize andrespond to oneanother withspecificity (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 cell Endorphin receptors (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.
A Chemical reaction Is the making and breaking of chemical bonds Leads to changes in the composition of matterChemical equilibrium Is reached when the forward and reverse reaction rates are equalIn the cell, enzymes make and break covalent bonds.Only in rare cases can a covalent bond be brokenwithout an enzyme.
Convert reactants to products + 2 H2 + O2 2 H2O Reactants Reaction Product No change inChemical equilibrium - concentration ofthe forward and reverse reactants orreaction rates are equal product.