Could the first steps of chemical evolution have occurred on ancient Earth?  To find out, Stanley Miller combined methane (CH 4 ), ammonia (NH 3 ), and hydrogen (H 2 ) in a closed system with water, and applied heat and electricity as an energy source.  The products included hydrogen cyanide (HCN) and formaldehyde (H 2 CO), important precursors for more- complex organic molecules and amino acids.  In more recent experiments, amino acids and other organic molecules have been found to form easily under these conditions.

Nonpolar side chains Polar side chains Electrically charged side chains Glycine (G) Gly Alanine (A) Ala Valine (V) Val Leucine (L) Leu Isoleucine (I) Ile Methionine (M) Met Phenylalanine (F) Phe Tryptophan (W) Trp Proline (P) Pro Serine (S) Ser Threonine (T) Thr Cysteine (C) Cys Tyrosine (Y) Tyr Asparagine (N) Asn Glutamine (Q) Gln AcidicBasic Aspartate (D) Asp Glutamate (E) Glu Lysine (K) Lys Arginine (R) Arg Histidine (H) His No charged or electronegative atoms to form hydrogen bonds; not soluble in water Charged side chains form hydrogen bonds; highly soluble in water Partial charges can form hydrogen bonds; soluble in water

 The 21 amino acids differ only in the variable side chain or R-group attached to the central carbon  R-groups differ in their size, shape, reactivity, and interactions with water. (1) Nonpolar R-groups: Do not form hydrogen bonds; coalesce in water (2) Polar R-groups: Form hydrogen bonds; readily dissolve in water  Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.

 A protein’s primary structure is its unique sequence of amino acids.  Because the amino acid R-groups affect a polypeptide’s properties and function, just a single amino acid change can radically alter protein function.

Normal amino acid sequenceSingle change in amino acid sequence Normal red blood cells Sickled red blood cells

 Secondary structure results in part from hydrogen bonding between the carboxyl oxygen of one amino acid residue and the amino hydrogen of another. A polypeptide must bend to allow this hydrogen bonding—thus,  - helices or  -pleated sheets are formed.  Secondary structure depends on the primary structure— some amino acids are more likely to be involved in α - helices; while others, in β -pleated sheets.  Secondary Structure increases stability by way of the large number of hydrogen bonds.

Hydrogen bonds form between peptide chains. Secondary structures of proteins result.  -helix  -pleated sheet  -helix  -pleated sheet Ribbon diagrams of secondary structure. Hydrogen bonds Arrowheads are at the carboxyl end of the arrows

 The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, and contribute to the 3D shape of the polypeptide.  R-group interactions include hydrogen bonds, van der Waals interactions, covalent disulfide bonds, and ionic bonds.  Hydrogen bonds can form between hydrogen atoms and the carboxyl group in the peptide-bonded backbone, and between hydrogen atoms and atoms with partial negative charges in side chains.

Interactions that determine the tertiary structure of proteins Hydrogen bond between side chain and carboxyl oxygen Hydrogen bond between two side chains Hydrophobic interactions (van der Waals interactions) Ionic bond Disulfide bond

Tertiary structures are diverse. A tertiary structure composed mostly of  - helices A tertiary structure composed mostly of  -pleated sheets A tertiary structure rich in disulfide bonds

 van der Waals interactions are electrical interactions between hydrophobic side chains. Although these interactions are weak, the large number of van der Waals interactions in a polypeptide significantly increases stability.  Covalent disulfide bonds form between sulfur- containing R-groups.  Ionic bonds form between groups that have full and opposing charges.

 Some proteins contain several distinct polypeptide subunits that interact to form a single structure; the bonding of two or more subunits produces quaternary structure.  The combined effects of primary, secondary, tertiary, and sometimes quaternary structure allow for amazing diversity in protein form and function.

Cro protein, a dimerHemoglobin, a tetramer

 Monosaccharide  Single sugar  Ex. Glucose, Fructose  Disaccharide  Two sugars  Ex. Sucrose, Lactose, Maltose

Linear form of glucoseRing forms of glucose  -Glucose  -Glucose Oxygen from the 5-carbon bonds to the 1-carbon, resulting in a ring structure

Figure 5-4 Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…  -Glucose …between various carbons and with various geometries.  -Galactose  -Glucose Lactose (a disaccharide) Maltose (a disaccharide) In this case, the hydroxyl groups from the 1-carbon and 4-carbon react to product a  -1,4-glycosidic linkage and water The hydroxyl groups from the 1-carbon and 4-carbon react to produce an  -1,4-glycosidic linkage and water

Figure 5-4a Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages…  -Glucose Maltose (a disaccharide) The hydroxyl groups from the 1-carbon and 4-carbon react to produce an  -1,4-glycosidic linkage and water

Figure 5-4b …between various carbons and with various geometries.  -Galactose  -Glucose Lactose (a disaccharide) In this case, the hydroxyl groups from the 1-carbon and 4-carbon react to product a  -1,4-glycosidic linkage and water

 Complex Carbohydrate ( Starch)  Ex. Starch, Cellulose, Chitin  More than one ring structure

Cellulose in plant cell wall Chitin in insect exoskeletonPeptidoglycan in bacterial cell wall

Figure 5-5a-Table 5-1

Figure 5-5b-Table 5-1

Figure 5-5c-Table 5-1

Outside of cell Inside of cell Glycoprotein

 Unsaturated  Comes from plants and is liquid at room temperature  Ex. Corn oil, Olive oil, Sunflower oil  Better for you  Saturated  Comes from animals and is solid at room temperature  Ex. Bacon, animal fat  Bad for you

DNA  Deoxyribonucleic Acid  Phosphate, Deoxyribose sugar, Nitrogen Base  Double sided  Helical Structure  Found in nucleus RNA  Ribonucleic Acid  Phosphate, Ribose sugar, Nitrogen Base  Single sided  Can be various places in the cell depending on type

Figure 4-1 Nucleotide Sugars Nitrogen-containing bases Phosphate group 5-carbon sugar Nitrogenous base RiboseDeoxyribose Cytosine (C) Uracil (U) Pyrimidines Thymine (T) Guanine (G)Adenine (A) Purines Only in RNA Only in DNA

Figure 4-2 Phosphodiester linkage Condensation reaction

Figure 4-3 The sugar-phosphate spine of RNA The sequence of bases found in an RNA strand is written in the 5´  3´ direction Nitrogenous bases 3´ and 5´ carbons joined by phosphodiester linkage Unlinked 3´ carbon: New nucleotides are added here

Figure 4-6b Hydrogen bonds form between G-C pairs and A-T pairs. GuanineCytosine ThymineAdenine Sugar-phosphate backbone Hydrogen bonds DNA contains thymine, whereas RNA contains uracil

Major groove Minor groove Length of one complete turn of helix (10 rungs per turn) 3.4 nm Distance between bases 0.34 nm Width of the helix 2.0 nm