Lecture Notes for Monday, September 21; BTNY 1210, Fall 1998

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Outline

Proteins

Nucleic Acids

PROTEINS

The subunits of proteins are amino acids and are easily recognized because each contains an amino group and a carboxyl group. There are 20 different amino acids, each of which contains this common "amino acid" structure, but differs in an "R" group or side chain. Examine Figure 2-15 and notice that some amino acids have nonpolar R groups that are hydrophobic (i.e. they lack nitrogen or oxygen), whereas others have charged or polar R groups that are hydrophilic (i.e. they contain nitrogen and oxygen). Two of the 20 amino acids have a sulfhydryl group (e.g. cysteine).

Amino acids are linked by a dehydration synthesis reaction resulting in a covalent bond between the amino group of one amino acid and the carboxyl group of another amino acid. Two amino acids linked together are called a dipeptide. A common dipeptide of the amino acids aspartic acid and phenylalanine is called aspartame and is sold as the low calorie sweetner Nutrasweet. The protein macromolecule (sometimes called a polypeptide) is typically composed of several hundred amino acids covalently linked together in a chain to form the primary structure of a protein. Examine Fig. 2-16 which shows 6 amino acids joined by covalent bonds; this is a small part of a protein. Just as we can form many different words by using 26 letters in various combinations, there are also a vast number of protein "words" that can be formed by using 20 different amino acid "letters" in different sequences.

Does the order of amino acids matter? YES! Why does the order matter? Just as each unique English word has a different meaning, each unique protein "word" has a different shape and therefore a different function. Changing one amino acid in a protein can result in loss of proper function - read about hemoglobin and sickle-cell anemia on page 223 in Lecture Supplement #4 for an example. How is the order determined? The information to produce the correct order of amino acids in a given protein is contained in DNA; protein synthesis will be considered later.

There are several levels of organization in the structure of a protein. The linear, primary structure of a protein coils and folds into a more compact and stable structure before it assumes its function. The secondary structure consists of coils and pleated sheets of the primary structure and is held together by hydrogen bonds between adjacent coils or side-by-side chains in the pleated sheet (examine Figs. 2-17 and 2-18). The amino acid R groups (side chains, shown in brown) stick out to the side of the coil and above or below the plane of the pleated sheet and therefore are not directly involved in the secondary structure. The tertiary structure of a protein involves a folding of the secondary structure (Fig. 2-19) and it is held together by several types of weak interactions (hydrogen bonds, hydrophobic interactions and S-S bonds) between R groups in various parts of the protein. Thus the positions of the R groups sticking out of the coil and sheet are determined by the positions of the particular amino acid "letters" in the protein "word" and determine how the protein will fold into its tertiary structure and therefore what its final shape will be. The shape (or tertiary structure) is what determines the specific function of the protein; a unique protein "word" results in a uniquely shaped (folded) protein with a unique function. Notice the association of structure and function.

Proteins whose tertiary shape is long and fibrous function as structural components such as tendons, muscles, hair, microtubules, actin filaments; you will recognize that some of these are more common in animals than in plants. Globular proteins often function as enzymes (the machinery of the cell), as transport proteins in membranes and as receptor molecules on the surface of cells helping cells recognize and communicate with each other.

NUCLEIC ACIDS consist of chains of subunits called nucleotides. Each nucleotide consists of three smaller subunits (Fig. 2-20): (l) a 5-carbon monosaccharide (either ribose or deoxyribose - see Fig. 2-21), (2) a phosphate group and (3) one of five ring-shaped, nitrogen containing molecules called nitrogenous bases. The nucleotides are joined together in the macromolecule (nucleic acid) so as to form an alternating sugar-phosphate backbone with the nitrogenous bases sticking out to one side.

Ribonucleic acid (RNA) contains the sugar ribose and the bases A, G, U and C and is single stranded. RNA functions in protein synthesis; certain RNA molecules form part of the ribosome and other RNA molecules carry the message for protein synthesis from the DNA in the nucleus to the ribosome in the cytoplasm.

Deoxyribonucleic acid (DNA) contains the sugar deoxyribose and the bases A, G, T and C. In the DNA molecule two single strands become attached to each other through hydrogen bonds between A and T and between G and C bases on the opposing strands to form a ladder-like molecule. Closely examine Fig.10-18 on page 200 noticing the sugar-phosphate backbone, the nitrogenous bases (thymine, cytosine, adenine and guanine) and the complementary fit between A and T and between G and C. The sugar-phosphate backbones of each strand form the vertical parts of the "ladder" and the A-T and G-C base pairs form the rungs of the "ladder". Furthermore, the whole DNA "ladder" is twisted along its long axis - see Fig. 10-17 on page 298. The DNA molecule measures approximately 2 nm from side to side. The structure of DNA was deduced in 1953 by James Watson and Francis Crick information provided by earlier studies of Linus Pauling, Rosalind Franklin, Maurice Wilkins and Erwin Chargaff (see pp. 197-199). The function of DNA is to store and replicate the genetic information in the cell; this information is encoded in the linear sequence of the bases along the DNA molecule. A typical eukaryotic chromosome contains approximately 70 million base pairs. The human genome (i.e. the DNA in 46 chromosomes contained in the nucleus of each and every human cell) contains approximately 6 billion base pairs.