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U-M BIOLOGY 172 - Macromolecules

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BIO 172January 14, 2019MacromoleculesReadings 2.5-2.6 and 4.11. Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units.2. Life likely originated on Earth by a set of chemical reactions that gave rise to the molecules of life.3. Proteins are linear polymers of amino acids that form three-dimensional structures with specific functions.2.5 Summary2.5 Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units.o Amino acids are linked by covalent bonds to form proteins. o An amino acid consists of a carbon atom (the α carbon) attached to a carboxyl group,an amino group, a hydrogen atom, and a side chain. o The side chain determines the properties of an amino acid. o Nucleotides assemble to form nucleic acids, which store and transmit genetic information. o Nucleotides are composed of a 5-carbon sugar, a nitrogen-containing base, and a phosphate group. o Nucleotides in DNA incorporate the sugar deoxyribose, and nucleotides in RNA incorporate the sugar ribose. o The bases are pyrimidines (cytosine, thymine, and uracil) and purines (guanine and adenine). o Sugars are carbohydrates, molecules composed of C, H, and O atoms, usually in the ratio 1:2:1, and are a source of energy. o Monosaccharides assemble to form disaccharides or longer polymers called complex carbohydrates. o Lipids are hydrophobic. o Triacylglycerols store energy and are made up of glycerol and fatty acids. o Fatty acids consist of a linear hydrocarbon chain of variable length with a carboxyl group at one end. o Fatty acids are either saturated (no carbon–carbon double bonds) or unsaturated (one or more carbon–carbon double bonds). o The tight packing of fatty acids in lipids is the result of van der Waals forces, a type of weak, noncovalent bond. 2.6 How did the Molecules of Life Form? The building blocks of life can be generated in the laboratory. Question: Could the building blocks of organic molecules have been generated on the early Earth? Background: In the 1950s, Earth’s early atmosphere was widely believed to have been rich in water vapor, methane, ammonia, and hydrogen gas, with no free oxygen. Experiment: Stanley Miller started with gases such as water vapor, methane, and hydrogen gas, all thought to have been present in the early atmosphere. He put these gases into a sealed flask and then passed a spark through the mixture.On the primitiveEarth, lightning might have supplied the energy needed to drive chemical reactions, and the spark was meant to simulate its effects.  Results: As the experiment proceeded, reddish material accumulated on the walls of the flask. Analysis showed that the brown matter included a number of amino acids. Conclusion: Amino acids can be generated in conditions that mimic those of the early Earth. Careful experiments have shown how polymers could have formed in the conditions of the early Earth.  Clay minerals that form from volcanic rocks can bind nucleotides on their surfaces. The clays provide a surface that places the nucleotides near one another, making it possible for them to join to form chains or simple strands of nucleic acid. 4.1 Molecular Structure of Proteins The exact order of amino acids in a protein determines the protein’s shape and function. The general structure of an amino acid consists of a central carbon atom, called the α (alpha) carbon, connected by covalent bonds to four different chemical groups, an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom (–H), and a variable side chain or R group.- In the environment of a cell, where the pH is in the range 7.35–7.45 (called physiological pH), the amino group gains a proton to become and the carboxyl group loses a proton to become –COO–). - The four covalent bonds from the α carbon are at equal angles. As a result, an amino acid forms a tetrahedron, a pyramid with four triangular faces- The R groups of the amino acids differ from one amino acid to the next. The R groups are chemically diverse and are grouped according to their properties, with a particular emphasis on whether they are hydrophobic or hydrophilic or have special characteristics that might affect a protein’s structure. These properties strongly influence how a polypeptide folds, and hence thethree-dimensional shape of the protein. Hydrophobic amino acids are those that do not readily interact with water or form hydrogen bonds.  Most hydrophobic amino acids have nonpolar R groups composed of hydrocarbon chains or uncharged carbon rings.  Because water molecules in the cell form hydrogen bonds with each other instead of with the hydrophobic R groups, the hydrophobic R groups tend to aggregate with each other.- The tendency for hydrophilic water molecules to interact with each other and for hydrophobic molecules to interact with each other is the very same tendency that leads to the formation of oil droplets in water. - This is also the reason why most hydrophobic amino acids tend to be buried in theinterior of folded proteins, where they are kept away from water. Amino acids with polar R groups have a permanent charge separation, in which one end of the R group is slightly more negatively charged than the other. Polar molecules are hydrophilic, and they tend to form hydrogen bonds with each other or with water molecules. The R groups of the basic and acidic amino acids are strongly polar.  At the pH of a cell, the R groups of the basic amino acids gain a proton and become positively charged, whereas those of the acidic amino acids lose a proton and become negatively charged. - Because the R groups of these amino acids are charged, they are usually located on the outside surface of the folded molecule. - The charged groups can also form ionic bonds with each other and with other charged molecules in the environment, in which a negatively charged group or molecule bonds with a positively charged group or molecule.  This ability to bind another molecule of opposite charge is one important way in which proteins can associate with each other or with other macromolecules such as DNA. The properties of several amino acids are noteworthy because of their effect on protein structure. These amino acids include glycine, proline, and cysteine.  Glycine is different from the other amino acids because its R


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U-M BIOLOGY 172 - Macromolecules

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