BIO-202 Exam 1 - Exam 1 notes PDF

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Chapter 2: The Chemical Context of Life ●

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Element ○ A pure substance made up of one kind of atom ■ atoms cannot be broken down into simpler substances because it is indivisible. ■ when atoms combine, they make molecules/compounds Atom ○ Made of subatomic particles: protons and neutrons (make up the atomic nucleus) ○ Electrons are in an orbit around the nucleus (not in the nucleus) ○ Atoms overall are neutral: # protons = # electrons ○ Atomic number = # protons (identifies the element) ○ Mass number (atomic weight) = # protons + # neutrons Isotopes ○ are variants of a particular chemical element which differ in neutron number, they differ in mass Orbital ○ Place, where the electrons are going to be at any given time. ○ A stable orbital contains 2 electrons (one pair) ○ 1st shell (1 orbital), 2/3rd shells (4 orbitals) Covalent Bond ○ The sharing of a pair of valence electrons by two atoms ○ It is the strongest bond (under physiological conditions) ○ Non-polar covalent bond ■ Bonding electrons shared equally between 2 atoms. No charge on atoms. ○ Polar covalent bond ■ Bonding electrons shared unequally between 2 atoms. Partial (+/-) charge on atoms ■ In a polar covalent bond, one atom is more electronegative, thus the electrons are shifted towards the nucleus of the more electronegative atom. ● Electronegativity ○ Is an atom’s attraction for the electrons. The more electronegative an atom is, the more strongly it pulls shared electrons towards itself. ● Oxygen (O-H) is the most polar covalent bond because it is the most electronegative. Hydrogen bond ○ It results from the attractive force between a hydrogen atom covalently bonded to a very electronegative atom such as an N, O, or F atom and another very electronegative atom.

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○ Is not a sharing of electrons, it is an attraction!!! ○ DNA is held together by hydrogen bonds. Ionic bond ○ Is a chemical bond that results from the attraction between oppositely charged ions ■ after the transfer of an electron, both atoms have charges and are called ions. ● Cation - positively charged ion ● Anion - negatively charged ion ○ Compounds formed through these are salts and found in nature as crystals

Chapter 3: Water and Life ●

Water is the biological medium on Earth ○ Water can interact with one another due to polarity and hydrogen bonding ■ Hydrogen bonding allows water to be cohesive (water molecule attracts water molecule), a  dhesive (attracts other polar covalent molecules), and gives s  urface tension (allows it to resist from outside external forces) ○ Water expands when freezing and floats, ( ice is less dense than water because the individual water molecules are further apart) ■ The hydrogen bonds in ice keep the water molecules farther apart than in liquid water. ○ Water has a high specific heat, which means that it can absorb or release a large amount of heat with only a slight change in its own temperature. (can be traced to hydrogen bonding) ■ Heat is a  bsorbed when hydrogen bond breaks (as water starts moving) ■ Heat is released when hydrogen bond forms (as the water stays still) ● Heat - a measure of the total amount of kinetic energy due to molecular motion ● Temperature - measures the intensity of heat due to the average kinetic energy of molecules ● Evaporation - is a mechanism adopted by organisms to let off heat through the water in hot temperatures ○ Water is an excellent solvent ■ Hydrophilic means that the substance dissolves easily in water ● Ionic compounds ○ break in water as the polar side of the water is attracted to the positive side of an ionic compound, while the negative side of an ionic compound is attracted to the positive part of the water ● Polar covalent substances ○ break down in the water as the molecules form hydrogen bonds with water molecules

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Water molecules exist in dynamic equilibrium where protons move from one molecule to another, to another in aqueous solutions. ○ Ex: H2O + H2O = H3O^+ + OH^pH defines the acidity of a solution. By concentration of hydronium ions (H3O^+) ○ 10^-7) , >7 = Basic ( RNA -> Proteins ● RNA is thought to be the first biological molecule (theory called RNA world) ○ Nucleic Acids are polymers of nucleotides ■ Nucleotides consist of a nitrogen base, five-carbon sugar (ribose), and one or more phosphate groups ● Base in carbon #1, phosphate in carbon #5 ■ B-D-ribose is used in RNA ■ B-D-2 deoxyribose is used in DNA, lacks hydroxyl group which makes DNA more secure ■ Bases fall into two classes, pyrimidine (single ring) and purine (double ring) ● Pyrimidine = uracil, cytosine, and thymine ● Purine = adenine and guanine ○ Phosphodiester linkage connects phosphate group linked to carbon #5 to the nearby carbon #3 sugar ■ All of the nucleotides are attached to each other through the covalent bond between 3’ hydroxyl and on 5’ phosphate of the incoming amino acid. ○ A and T, G and C ○ DNA runs antiparallel which means that two complementary strands run in opposite directions to match ■ the 5’ to 3’ direction of one strand is opposite to the complementary strand, oriented in a 3’ to 5’ direction. ○ Structure of DNA proposed by Watson and Crick in 1953...