The Chemical Context of Life Chemical Basis of Biology.
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The Chemical Context of Life Chemical Basis of Biology
Elements : Matter : made up of elements, substances that cannot be broken down to other substances by chemical reactions Compounds Molecular Atom
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 The atomic number of an element – Is the number of protons – Is unique to each element
Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar The periodic table of the elements
A few other elements –Make up the remaining 4% of living matter major elements Essential Elements of Life (25/92) O, C, H, N (96%) Trace elements (<0.01%)
(a) Nitrogen deficiency (b) Iodine deficiency The effects of essential element deficiencies 0.15mg/per day
Neutrons: no electrical charge Protons: positively charged Electrons: negatively charged Atoms Nucleus Cloud of negative charge (2 electrons) Electrons orbital Valence electrons Are those in the outermost, or valence shell Determine the chemical behavior of an atom
Isotopes differ in the number of neutrons same number of protons Radioactive isotopes –Spontaneously give off particles and energy 32 P 3H3H 14 C
Incubators Human cells 12 3 456 987 10°C 15°C20°C 25°C 30°C35°C 40°C 45°C 50°C DNA (old and new) 1 2 3 4 5 6 7 8 9 Radioactive isotopes Ingredients including Radioactive tracer (bright blue) 3H3H scintillation fluid Whether temperature affects the rate of DNA synthesis?
Nitrogenous base Nucleoside O O OO OO P CH 2 5’C 3’C Phosphate group Pentose sugar O H RNA DNA -OH 32 P 3 H 14 C
Temperature (°C) 102030 4050 Optimum temperature for DNA synthesis 30 20 10 0 Counts per minute (x 1,000) scintillation counter *DNA ( 3 H) Temperature affects the rate of DNA synthesis —the most DNA was made at 35°C.
–Can be used in biology Cancerous throat tissue Radioactive isotopes *glucose
SodiumChloride (Cl) Sodium Chloride + ionic compounds (or salts) – two or more elements combined in a fixed ratio – In nature as crystals of various shape and size (see fig2.14) NaCl (Na) – characteristics different from those of its elements
– Na Cl + Cl – Chloride ion (an anion) Na Sodium atom Cl Chlorine atom Na + Sodium on (a cation) Sodium chloride (NaCl) –an attraction between anions and cations –Environment affects the strength of ionic bonds ionic bond in compound An anion: negatively charged ions A cation: positively charged ion
(c) Methane (CH 4 ). Water (H 2 O). (d) H O H HH H H C Covalent bond in compounds -sharing of a pair of valence electrons
In a nonpolar covalent bond – The atoms have similar electronegativities – Share the electron equally Hydrogen (H 2 ). Oxygen (O 2 ). HH O O
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 O2O2 The most electronegative of the 92 elements:
H2OH2O –– O H H ++ ++ In a polar covalent bond The atoms have differing electronegativities Share the electrons unequally ( O>H ) Delta minus Delta plus Partial negative Partial positive
Weak chemical bonds are important in living systems Hydrogen Bonds Van der Waals Interactions ReversibilityInter-molecular interaction: Intra-molecular interaction in the large biological molecular ex. Protein Ionic bond (3D structure)
Hydrogen Bonds – – + + + + Water (H 2 O) Ammonia (NH 3 ) O H H + + – – N H H H ++ d+d+ When a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom Partial positive charge Partial negative charge H ….. O H ….. N Insects walk on water.
Van der Waals Interactions Help molecules adhere to each other Weak Occur only when atom and molecular are very close together Occur when transiently positive and negative regions of molecules attract each other Gecko lizard Tiny hairs Increase surface area
Molecular Shape and 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
Electron Orbitals An orbital – Is the three-dimensional space where an electron is found 90% of the time Each electron shell – Consists of a specific number of orbitals 1s orbital2s orbitalThree 2p orbitals1s, 2s, and 2p orbitals (a) First shell (maximum 2 electrons) (b) Second shell (maximum 8 electrons) (c) Neon, with two filled shells (10 electrons) x Z Y
s orbital Z Three p orbitals X Y Four hybrid orbitals Tetrahedron In a covalent bond The s and p orbitals may hybridize, creating specific molecular shapes Molecular Shape and Function determined by the positions of its atoms’ valence orbitals
Space-filling model Hybrid-orbital model (with ball-and-stick model superimposed) Unbonded Electron pair 104.5° O H Water (H 2 O) Methane (CH 4 ) H H H H C O H H H C Ball-and-stick model H H H H The positions of the hybrid orbital determine the shapes of the molecules
Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Natural endorphin Natural endorphin Endorphin receptors Morphine Brain cell specificity Structures of endorphin and morphine drugs Molecular Shape and Function
Reactants Reaction Product 2 H 2 O2O2 2 H 2 O + + – Convert reactants to products Reactants – making and breaking of chemical bonds – changes in the composition of matter A chemical reaction
Photosynthesis 6CO 2 + 6H 2 O C 6 H 12 O 6 + O 2 glucose Sunlight
the forward and reverse reaction rates are equal Chemical equilibrium dynamic process 3H 2 + N 2 2NH 3 reversible Relative concentration of product and reactants stop to change