Bio 1201 Chapter 2 The Chemical Context of Life Organisms are composed of matter which is anything that takes up space and has mass Matter is composed of elements An element is a substance that cannot be broken down to other substances by chemical reactions Essential Elements of Life 4 elements make up about 96 of living matter Carbon Hydrogen Oxygen Nitrogen Concept 2 2 An element s properties depend on the structure of it s atoms An atom is the smallest unit of matter that still retains the properties of an element Composed of even smaller untis of matter called subatomic particles Subatomic Particles Proton 1 unit of postive charge Electron 1 unit of negative charge Neutron no charge Protons and neutrons are packed together tightly in the nucleus at the center of an atom Electrons exsist in a cloud of negative charge surrounding the nucleus Atomic Numbers The atomic number is the number of protons in the nucleus The atomic mass number is the total number of protons and neutrons in the nucleus Isotopes are atoms of the same element with different numbers of neutrons Electron Distribution Chemical Properties The chemical behavior of an atom is determined by the distribution of electrons in the atom s electron shells mostly the outermost shell Called valence electrons Valence is the number of chemical bonds that an atom will form Atoms in Living Systems their valence Hydrogen 1 Oxygen 2 Nitrogen 3 Carbon 4 all in outershell Concept 2 3 The formation and function of molecules depend on chemical bonding between atoms Atoms with incomplete valence shells can interact with other atoms with incomplete valence shells Can result in either the sharing or transfer of electrons in the formation of chemical bonds An atom with an incomplete partially full electron shell is reactive where as an atom with a full electron shell is inert or not chemically active Example The Hindenburg 1937 Covalent Bonds Involves the sharing of a pair of valence electrons by two atoms Strongest electrons by two atoms 83 Kcal mol Example 2 hydrogen atoms Single valence electron is held in its orbital by its attraction to the proton in the nucleus When 2 hydrogen atoms approach each other the electron is also attracted to the proton in the neighboring nucleus The 2 electrons become shared in the form of a covalent bond Electronegativity really positive An atom s capacity to attract and hold electrons within a covalent bond The more electonegativity an atom has the more strongly it attracts electrons towards itself Relative electronegativity is what determines the polarity of a molecule Non polar Covalent bonds C C bonds electonegativity is identical C H bonds electonegativity is very close 2 6 2 2 O O bonds electonegativity is identical These are non polar covalent bonds because the bonded atoms have similar or identical electonegativity and the bonding electrons are shared equally Logic flow 1 No difference in electrons 2 Electrons are equally shared between atoms 3 Bond is non polar no dipole moment 4 Which makes it hydrophobic Polar Covalent bonds Atoms making up the bond are significantly different in their electonegativity There is an unequal sharing of the electrons For example the water molecule H O H Bonds of this type are generally hydrophilic in nature Ionic Bonds Occurs when 2 atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron from another atom Most common example is sodium chloride Moves one unit of negative charge 1 electron from sodium to chloride Sodium is a cation After donating one electron it still has 11 protons but now has only 10 electrons Now has a charge of 1 Chlorine is an anion It gains an electron giving it 18 electrons but still only 17 protons Now has a negative charge of 1 Hydrogen Bonds Normally hydrogen forms a covalent bond with only one other atom HOWEVER hydrogen can form an additional weak association a hydrogen bond with another electronegative atom usually Nitrogen or Oxygen Definition is in 2 parts A hydrogen atom is covalently bonded to a more electronegative atom oxygen such that the bond is polar R O negative H positive N negative H 3 4 2 2 3 0 Part 2 Van der Waals interactions Then another electronegative atom nitrogen is attracted to the hydrogen by opposing charges Non specific weak interactions between two closely spaced atoms Occur due to random fluctuations in electron distributions around the atoms involved Such that a transient dipole exists between the two atoms Transient dipole a temporary separation of equal and opposite partial charges within a region of a molecule Apply to both non polar and polar molecules If the atom gets too close their outermost electron repels each other Van der Waals Forces This will cause the electrons of one of the atoms to shift forming a transient dipole in one of the atoms Then the 2 dipoles will attract each other weakly due to Van der Waal s forces Weaker than hydrogen bonds but like H bonds Van der Waals interactions can be accumulation to help stabilize macromolecular structure Recently shown to be responsible for the gecko s ability to walk up a wall Each gecko toe has thousands of tiny hairs The Van der Waal s interactions between the hair tip molecule and the molecules of a wall s surface are so numerous that they can accumulate and support the gecko s body weight Molecular Shape and Function Molecules have characteristics size and shape Shape is very important to its function in the living cell o Form dictates function o Determines how biological molecules recognize and respond to each other with specificity Molecular Specificity morphine Opiates are drugs derived from opium During the 1800s morphine was derives from opium and heroin was synthesized from Blind opiate receptors in the brain Class of chemical called endorphins were discovered in 1975 Signaling molecules made by the pituitary gland during times of intense stress or excessive exercise o Nature s plain relievers o Opiates are similar in shape to endorphins and mimic their action by binding to endorphin receptors in the brain
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