Amino Acids & Proteins

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1 Chemistry 131 Lecture 13: Protein Function; Amino Acids and Properties, Chirality & Handedness in Amino Acids, Primary Protein Structure Sections in McMurry, Ballantine, et. al. 7 th edition Introduction Amino Acids & Proteins As we move into our introductory study of biochemistry, we should bear in mind the fundamental building block in biology, the cell: Though a bit simplistic, a good way to think of how cells function is that information for generating particular proteins and the structure and capacity for executing a variety of tasks is encoded in the DNA. Expression of particular proteins allows cells to become specialized for a given task (e.g. muscle contraction). In the eukaryotic (animal) cell, the DNA and the protein it codes for is localized in the nucleus, and must be copied (as mrna) in order to be shipped out to the ribosomal protein factory (located on the endoplasmic reticulum, giving it a rough appearance) in order to make the working protein. So what are the functions carried out by proteins? You name it! 1

2 Uses of Proteins: 1. Structural. In animals, the main structural material is protein; in particular collagen and keratin Collagen forms an unusual triple helix refer to figure 18.9 Collagen + hydroxyapatite (Ca 5 (PO 4 ) 3 OH) = bone Keratin is another fibrous protein that forms filaments and is the main component of claws, fingernails, hair and horn 2. Chemical Catalysis. The overwhelming majority of reactions in the body are catalyzed by proteins. Catalytic proteins are termed enzymes. Using catalytic proteins offers a variety of means of control including phosphorylation (carried out by kinases) or dephosphorylation (carried out by phosphatases) 3. Movement. Muscle is composed of actin and myosin 4. Molecular Transport. O 2 is transported by hemoglobin, Fe by transferritin, non-polar steroid hormones by carrier proteins. There are also numerous membrane embedded protein channels which allow the passage of ions and polar organic molecules through cellular membranes 5. Hormones/Cellular Communication. Most of the hormones produced by the body are protein/peptide hormones, such as angiotensin, insulin, all of the the hypothalamic/pituitary hormones (table 20.1) and the ever popular enkephalins and endorphins (section 20.10) 6. Protection. Antibodies are proteins that figure prominently in defense of the host 7. Nutrient Storage. Casein, ovalbumin provide energy for developing mammals and birds, respectively 8. Regulation of Gene Expression. Perhaps the most important function of proteins is the regulation of the genome; not only do proteins control the expression of genes, the sequential expression of proteins ultimately acts as a clock for the development and senescence of an organism As long as we were just referring to eggs (ovalbumin), the regulation of gene/protein expression by proteins is quite possibly the greatest chicken and egg question in existence 2

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4 Notice that in the broadest sense, the 3 main categories describing the function of proteins (in terms of variety, not total mass) are 1. Nucleic acid binding proteins control of the expression of other proteins 2. Enzymes control of the chemical reactions occurring inside (and outside) the cell 3. Signal transduction allow chemical signals to be generated and received between cells. Cellular communication is critical to orchestrating the functions that must occur in complex organisms such as the human being 4

5 Amino Acids Before we can talk about proteins, we must learn the alphabet Below is the general structure of an amino acid, shown as a Fischer projection, with the [most oxidized] carboxyl group on top and the amino group pointing to the left (L) or right (D). This is another way of assigning absolute configuration, just like the (R,S) system CO 2 H CO 2 H N H 2 R H = H 2 N C H R The question then becomes Do we use D, L, or both versions of an amino acid in order to make proteins? Answer: Question: Referring to table 18.3, which amino acid is not chiral? Answer: Non-polar, Polar neutral, Acidic and Basic Amino acids Please refer to table 18.3 When we talk about the making of proteins from amino acids, the amino group on one amino acid condenses with the carboxylic acid group on another amino acid, forming the peptide backbone. Consequently, to differentiate between amino acids in terms of polarity, focus only on the side chain This would probably be a good time to start memorizing the 3 letter abbreviations for the amino acids Amino Acids as Zwitterions Amino acids have an acidic and basic functional group on the same molecule; as a result, Amino acids are high melting solids ( o C) Amino acids are soluble in water 5

6 So what is occurring? An internal acid-base reaction! Amino acids in basic media: Amino acids in acidic media: Amino Acids and the Isoelectric Point (pi) pi may be defined as the ph at which amino acids cease to move in an electric field (when they have no net charge). The amino acid with the highest isoelectric point is the most basic amino acid arginine (pi = 10.76). Here s why: Question: What 2 amino acids would be the best candidates for lowest isoelectric point? Answer: All of the non-ionized amino acids (except cysteine) have 5.4 < pi < 6.5. Peptides Since amino acids contain both an amino and carboxyl group, 2 amino acids can condense and form an amide linkage When 2 amino acids do this it is referred to as a peptide bond The result of 2 amino acids condensing is a dipeptide, the result of 3 condensing is a tripeptide Polypeptides are strings of amino acids < approximately 30 amino acids Amino acids in a protein are often referred to as residues and are numbered from the N-terminus (as the N-terminus indicates where protein synthesis begins as we will discuss below) Obviously, order is important here, and the number of potential isomers increases exponentially with the number of amino acids 6

7 From Amino Acids to Peptides and Proteins, a Perspective: Gly + Gly Gly-Gly Gly + Ala Gly-Ala, Ala-Gly # isomers = 2 Gly + Ala + Val Gly-Ala-Val, Gly-Val-Ala, Ala-Gly-Val, Val-Gly-Ala, Ala-Val-Gly, Val-Ala- Gly # isomers = 6 Gly + Ala + Val + Leu Gly-Ala-Val-Leu, Gly-Ala-Leu-Val, Gly-Val-Ala-Leu, Gly-Leu-Ala-Val, Gly-Val-Leu-Ala, Gly-Leu-Ala-Val, x-gly-x-x(6), x-x-gly-x(6), x-x-x-gly(6) # isomers = 24 By 10 amino acids, 3,628,800 possible combinations Large proteins can contain up to 2,000 residues (myosin heavy chain, rabbit), so the possible combinations are virtually limitless When considering the condensation of amino acids to peptides (catalyzed at the ribosomal complex in the body), it is easier to view the unionized forms reacting: Having both an amino group and a carboxyl group allows amino acids to form condensation polymers, spitting out water as the good leaving group. As we know from our study of amides, water can attack the carbonyl of the amide/peptide linkage and break down proteins (heat and acid in the lab, digestive proteolytic enzymes in the body) into amino acids which can then be used for energy or the making of new proteins In reality, with blood ph = 7.4, amino acids exist in the zwitterionic state, which would make direct amide formation impossible (no lone pair of electrons on the now positive N, and lots of extra negative charge on the carboxylate group, making it unattractive to nucleophiles. So how does the cell get around this problem? First the amino acid is activated by coupling it to ATP, which allows the amino acid to be easily transferred to the correct trna (transfer ribonucleic acid) 7

8 The Activation of Amino Acids and the Formation of trna Amino Acid Esters Generation of Hot AMP-Amino Acid ATP + Amino Acid AMP-amino acid phosphoester + PP i Notice that this is an enzyme catalyzed reaction that generates an acid anhydride The subsequent hydrolysis of PP i drives the reaction The hot AMP-Amino Acid is then attached to a specific trna via a specific aminoacyl-trna synthetase Question: What is the nucleophile in the attachment of the trna to the amino acid? Answer: The 3 hydroxyl group on the last base in the trna Question: What is the second genetic code? Answer: The binding of a particular amino acid to the appropriate trna. If this gets screwed up, the cell is in big trouble - there is no proofreading function in the formation of the t-rna amino acid ester (unlike the proofreading that occurs in DNA replication). The aminoacyl t-rna synthetase has to get it right. Notice that once we have the amino acid carried into the ribosomal complex aka protein factory - it is a simple matter to form the peptide [amide bond] when the next amino acid bound trna is carried into the ribosomal complex and binds right next to the first. A swap of an amide for an ester then ensues. 8

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