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- NitrogenConcept 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 particlesSubatomic 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 nucleusAtomic 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 formAtoms 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 activeExample: The Hindenburg – 1937Covalent 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 bondElectronegativity (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 moleculeNon-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 equallyLogic flow: 1. No difference in electrons2. Electrons are equally shared between atoms3. Bond is non-polar (no dipole moment)4. Which makes it hydrophobicPolar 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 moleculeH-O-H- Bonds of this type are generally hydrophilic in natureIonic 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 -1Hydrogen 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) ³Part 2:- Then another electronegative atom (nitrogen) is attracted to the hydrogen by opposing chargesVan der Waals interactions- 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 atomsTransient 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 otherVan 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 thehair 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 cello Form dictates functiono Determines how biological molecules recognize and respond to each other with specificityMolecular Specificity- Opiates are drugs derived from opium- During the 1800s, morphine was derives from opium, and heroin was synthesized from morphine- 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 relieverso Opiates are similar in shape to endorphins and mimic their action by binding to endorphin receptors in the
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