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Western University
Biology 1002B
Tom Haffie

Lecture 1▯ • A photon can only be absorbed by an electron of a molecule only if the photon energy equal the energy difference between the electron’s ground state and its excited state▯ • If it is not absorbed, it is transmitted or reflected▯ • Carbon atoms in pigments are covalently bonded to each other with alternating single and double bonds – called a conjugated system – delocalized electrons▯ o Delocalized electrons are not associated with a particular atom or involved in bonding are available to interact with a photon of light▯ o Allows pigments to absorb light▯ • A pigment’s colour is the result of photons of light that it does not absorb, but instead these photons are reflected off or transmitted through the pigment to reach your eyes▯ ▯ Lecture 2▯ No ISOs assigned▯ ▯ Lecture 3▯ • General structure of an amino acid: central carbon atom attached to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom, and one of twenty different side groups represented by R▯ • The different side groups give amino acids their different properties▯ • The different classes of amino acids are:▯ o Nonpolar amino acids▯ o Uncharged polar amino acids▯ o Negatively charged (acidic) polar amino acids▯ o Positively charged (basic) polar amino acids▯ • A peptide bond joins amino acids together in a polypeptide chain▯ o Formed by dehydration synthesis between the amino group at one end and a carboxyl group at the other end▯ o Amino acids are added only to the carboxyl end of the growing peptide strand▯ • A polypeptide and a protein are different because a polypeptide is just a string of amino acids whereas a protein is a polypeptide that has folded into a specific three-dimensional shape▯ • Four levels of structure of a protein:▯ o Primary structure: a polypeptide chain; the complete amino acid sequence▯ o Secondary structure: polypeptide chain in a coil, regions of alpha helix and beta strand▯ o Tertiary structure: folding of coils – overall three dimensional shape of a protein▯ o Quaternary structure: arrangement of polypeptide chains in a protein that is formed from more than one chain▯ • Secondary structure is formed by hydrogen bonds between the hydrogen atom attached to the nitrogen of the backbone and the oxygen attached to one of the carbon atoms of the backbone▯ • Tertiary Structure is formed by ionic bonds, hydrogen bonds, hydrophobic interactions, and disulfide bridges. Tertiary structure is flexible, allowing conformational changes▯ • Alpha helixes are formed when hydrogen bonds form between every N-H group of the backbone and the C—O group of the amino acid▯ • Beta sheets are formed by the side-by-side alignment of beta strands▯ o Hydrogen bonds form between atoms of each strand, forming the sheet▯ ▯ Lecture 4▯ • Isolated system: one that does not exchange matter or energy with its surroundings▯ • Closed system: can exchange energy but not matter▯ • Open system: both energy and matter can move freely between the system and its surroundings▯ • First law of thermodynamics (principle of the conservation of energy): energy can be transformed from one form into another or transferred from one place to another, but it cannot be created or destroyed▯ • Second law of thermodynamics: the total disorder of a system and its surroundings always increases▯ o Systems will move spontaneously towards arrangements with greater entropy▯ It takes energy to maintain low entropy▯ o • Living cells are open systems – they bring in energy and matter and use them to generate order out of disorder – ie we eat food in order to maintain low entropy▯ • We take in ordered matter and convert it into highly disorder products such as CO2, increasing the entropy of our surroundings▯ • The entropy of a system such as an organism is allowed to decrease as long as the entropy of the universe as a whole increases▯ • Living organisms can be thought of as islands of low entropy in a sea that is constantly becoming more disordered▯ Lecture 5▯ • Fluid mosaic model:▯ Proteins within a mixture of lipid molecules the consistency of olive oil▯ o o It is important that the membrane stays fluid – has mechanisms to keep it this way▯ o Lipid bilayer▯ o The lipid molecules move around within the same bilayer half – making them highly dynamic▯ o Contain an assortment of different types of proteins ▯ o Proteins and other components of one half of the bilayer are different than those that make up the other half▯ ▪ Membrane asymmetry: reflects differences in the functions performed by each side of the membrane▯ • A lipid is a diverse group of water-insoluble molecule made up of mostly carbon and hydrogen – derived from isoprene and fatty acids▯ • A fatty acid consists of a single hydrocarbon chain with a carboxyl group linked at one end▯ • A phospholipid consists of a head group attached to two long chains of carbon and hydrogen called a fatty acid▯ • The head group consists of glycerol linked to one of several types of alcohols or amino acids by a phosphate group▯ • Phospholipids are amphipathic: has regions that are hydrophobic (tails) and hydrophilic (heads)▯ • Hydrophobic effect: the tendency of polar molecules like water to exclude hydrophobic molecules such as fatty acids▯ o Results in formation of lipid molecules in structures where the fatty acid tails interact with each other and the polar head groups associate with water▯ • Saturated: all the carbons are bou
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