So where were we? But what does the order mean? OK, so what's a protein? 4/1/11

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1 So where were we? We know that DNA is responsible for heredity Chromosomes are long pieces of DNA DNA turned out to be the transforming principle We know that DNA is shaped like a long double helix, with two strands held together by hydrogen bonds between complementary bases We know that DNA is a double polymer of nucleotides arranged in a complex order There s something critically important about the order that the nucleotides are in. In fact, it is now possible to sequence DNA -- to literally read off the order of nucleotides on a DNA strand. (This is what the famous Human Genome Project was about.) 1 cagctggggg taaggggggc ggattattca tataattgtt ataccagacg gtcgcaggct 61 tagtccaatt gcagagaact cgcttcccag gcttctgaga gtcccggaag tgcctaaacc 121 tgtctaatcg acggggcttg ggtggcccgt cgctccctgg cttcttccct ttacccaggg 181 cgggcagcga agtggtgcct cctgcgtccc ccacaccctc cctcagcccc tcccctccgg 241 cccgtcctgg gcaggtgacc tggagcatcc ggcaggctgc cctggcctcc tgcgtcagga 301 caagcccacg aggggcgtta ctgtgcggag atgcaccacg caagagacac cctttgtaac 361 tctcttctcc tccctagtgc gaggttaaaa ccttcagccc cacgtgctgt ttgcaaacct 421 gcctgtacct gaggccctaa aaagccagag acctcactcc cggggagcca gcatgtccac 481 tgcggtcctg gaaaacccag gcttgggcag gaaactctct gactttggac aggaaacaag 541 ctatattgaa gacaactgca atcaaaatgg tgccatatca ctgatcttct cactcaaaga 601 agaagttggt gcattggcca aagtattgcg cttatttgag gagaatgatg taaacctgac 661 ccacattgaa tctagacctt ctcgtttaaa gaaagatgag tatgaatttt..... But what does the order mean? To understand this, we have to study a second major class of biological molecules: proteins. Each and every living cell must make thousands of different proteins to carry out its life activities. These include: structural proteins (e.g. collagen, keratin) mobile proteins (e.g. actin and myosin in muscle) enzymes (proteins that drive chemical reactions, such as food digestion) signaling proteins (e.g. insulin) transport proteins (e.g. hemoglobin) and more! Lots more! OK, so what's a protein? Proteins are polymers of amino acids. There are twenty different amino acids that are used to make up proteins. The order that the amino acids are arranged in ultimately determines the protein's shape......and the shape of the protein is critical for determining what the protein does. 1

2 So what s an amino acid? Some of the twenty main amino acids... An amino acid has three major parts: the amino group the carboxyl group the R group Different amino acids have different R groups, but all have amino and carboxyl groups More of the twenty main amino acids... And yet more of the twenty main amino acids! (In all of these diagrams, the R groups are shaded. You do not need to memorize these amino acids!) 2

3 Amino acids bond together between the amino group of one amino acid, and the carboxyl group of another. This is a peptide bond. Chains of amino acids can be strung together using a series of peptide bonds. So what s an amino acid? Levels of Protein Structure Primary structure the order in which amino acids are put together Secondary structure folding of the amino acid chain (or polypeptide), caused by attraction between electrically charged atoms Tertiary structure further folding caused by attraction and repulsion between R-groups Quaternary structure several amino acid chains fitting together into one molecule Primary structure just refers to the order in which amino acids are strung together. Here s a stick-model of what a simple amino acid polymer looks like. (A single polymer of amino acids is often called a polypeptide, or just a peptide for short, by the way.) The primary structure of the human protein insulin looks like this... boring, ain't it? METHIONINE - ALANINE - LEUCINE - TRYPTOPHAN - METHIONINE - ARGININE - LEUCINE - LEUCINE - PROLINE - LEUCINE - LEUCINE - ALANINE - LEUCINE - LEUCINE - ALANINE - LEUCINE - TRYPTOPHAN - GLYCINE - PROLINE - ASPARTIC ACID - PROLINE - ALANINE - ALANINE - ALANINE - PHENYLALANINE - VALINE - ASPARAGINE - GLUTAMINE - HISTIDINE - LEUCINE - CYSTEINE - GLYCINE - SERINE - HISTIDINE - LEUCINE - VALINE - GLUTAMIC ACID - ALANINE - LEUCINE - TYROSINE - LEUCINE - VALINE - CYSTEINE - GLYCINE - GLUTAMIC ACID - ARGININE - GLYCINE - PHENYLALANINE - PHENYLALANINE - TYROSINE - THREONINE - PROLINE - LYSINE - THREONINE - ARGININE - ARGININE - GLUTAMIC ACID - ALANINE - GLUTAMIC ACID - ASPARTIC ACID - LEUCINE - GLUTAMINE - VALINE - GLYCINE - GLUTAMINE - VALINE - GLUTAMIC ACID - LEUCINE - GLYCINE - GLYCINE - GLYCINE - PROLINE - GLYCINE - ALANINE - GLYCINE - SERINE - LEUCINE - GLUTAMINE - PROLINE - LEUCINE - ALANINE - LEUCINE - GLUTAMIC ACID - GLYCINE - SERINE - LEUCINE - GLUTAMINE - LYSINE - ARGININE - GLYCINE - ISOLEUCINE - VALINE - GLUTAMIC ACID - GLUTAMINE - CYSTEINE - CYSTEINE - THREONINE - SERINE - ISOLEUCINE - CYSTEINE - SERINE - LEUCINE - TYROSINE - GLUTAMINE - LEUCINE - GLUTAMIC ACID - ASPARAGINE - TYROSINE - CYSTEINE - ASPARAGINE 3

4 Secondary structure is created when certain atoms in nearby amino and carboxyl groups, relatively close to each other, attract each other and cause the chain of animo acids to fold. Alpha-helices result when a chain of amino acids folds into a spiral. (Don t confuse this with the double helix of DNA!) Secondary structure: Beta-sheets result when a chain of amino acids folds back and forth into a pleated sheet. Tertiary structure is created when attractions and repulsions between R-groups cause further folding. This is the tertiary structure of a protein (human myoglobin, found in muscles) that happens to consist of several alpha-helices... And this is the tertiary structure of a protein (from cells in the intestine) that happens to consist of several betasheets wrapped around each other... 4

5 But most proteins, like this triose isomerase, consist of both alpha-helices (red) and beta-sheets (green). Here are yet more examples of tertiary structure(alphahelices are in blue, beta-sheets are in red)... Quaternary structure describes several polypeptides, each with its own tertiary structure, joining together. Another example of quaternary structure: one peptide chain is in blue and the other s in green. 5

6 And the point is...? Yet another example of quaternary structure: this protein (seen from two angles) happens to consist of seven separate polypeptides (each of which is colored differently). An organism makes a huge number of types of protein, which do an enormous number of things. The function of a protein depends on its shape. Heat, acid, and other factors may change the shape or protein molecules. This is called denaturing the protein. Denaturing a protein affects the protein's function (usually by making it non-functional). The shape of a protein depends on the order of its amino acids. And the point is...? In the 1900s, Archibald Garrod proposed what we now call the one gene, one protein hypothesis. A gene carries the instructions needed to assemble one protein. (More accurately: one polypeptide chain recall that many proteins are actually made of several chains.) The instructions are encoded in the order of DNA bases this is the genetic code. 6