Proteins : the basis of life diversity

1. Proteins: the basis of life diversity • Proteins are a class of diverse macromoleculesthat determine many characteristics of cells and, in turn, of the whole organisms. • All proteins are polymers constructed of subunits called amino acids. There are 20 types of amino acids in protein. Thus, the biological language expressed in proteins is a huge vocabulary of a complex words based on an alphabet (these 20 amino acids). The meaning of a protein rests in the exact order of its amino acids. The order gives the molecules its special characteristics as a structural component in a cell, as an enzyme, as a carrier, or whatever. In each amino acid there are one central carbon atom, bound to a hydrogen atom, and amino group (NH2), a carboxyl group (-COOH-), and a side chain, represented by R-group. R - group can be as simple as a single hydrogen atom, or as complex as the double ring structure. Some amino acids side chains are hydrophobic; and the other are ambivalent.

2. Proteins • Monomer – Amino Acids • Polymer – Polypeptide (a long string) • Proteins are the 3D structures formed • by one or more folded polypeptides • working together There are about 20 common amino acids that can make thousands of different kinds of proteins.

3. Characteristics of Amino Acids • Backbone is always the same • Side chains can be • Polar—hydrophilic • Nonpolar—hydrophobic • Acidic • Basic • Contain Sulfur (cysteine)

4. 6.3 Section Summary 6.3 – pages 157-163 Proteins • Peptide bonds – covalent bonds formed between amino acids.

5. 6.3 Section Summary 6.3 – pages 157-163 Proteins • A is a large, complex polymer composed of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. protein

6. Like polysaccharides, proteins are polymers, but the amino acid subunits are linked covalently by peptide bonds. The bonds are the result of a condensation reaction between the carboxyl group of one amino acid and the amino group of another. Two joined amino acid units are called dipeptide. A third amino acid can be joined by the other condensation reaction, to form tripeptide. The condensation reaction occurs again and again, forming chains that are typically 50 to hundreds of amino acids long. These polymer chain are called polypeptides, and regardless of length, each chain will have an amino terminus and a carboxyl terminus. A protein molecule can consists of one, two or several polypeptide chains bound to one another in various ways.

7. A second type of covalent bound called disulfide bond or bridge (-S-S-) results from linking of two sulfhydryl groups. These bonds can cause a kink or loop in a chain and join two polypeptide chains into one molecule. • In the early 1950s, Frederick Sanger of Cambridge University made one of the greatest discoveries in the history of biology by exploring the precise amino acid sequence of the protein hormone called insulin. The work of Sanger and his colleagues revealed than the order of amino acids is the key to the structure and function of proteins and that a specific sequence characterizes each type of protein.

8. Protein Structure • Primary Protein Structure – the order of amino acids in the polypeptide chain. Primary structure –the linear sequence of amino acids in a protein is referred to as its primary structure. Whether a protein functions as an enzyme, a hormone, or a structural component of a cell depends on its primary structure.

9. What determines the amino acid sequence? • The amino acid sequence is determined by information coded in that organism’s DNA http://science.csumb.edu/~hkibak/241_web/index.html

10. Secondary structure – the sequence of amino acids in a long polypeptide determines not just the biological meaning of the protein ‘word’, but the way the chains twists, bends, and folds into a characteristics of a series of high – order configurations called secondary, tertiary, and quaternary structure, which ultimately determine the protein’s activity in a living thing. The works of chemists L. Pauling and R, Corey helped reveal this hierarchy of protein structure and function by focusing on the spatial relationships of amino acids in polypeptide chains. They proved that the subunits of some proteins tend to occur in regularly repeating patterns and these patterns form the secondary structure of the protein.

11. Secondary Protein Structure • 3D shape starts to form • The amino acids in some proteins are stabilized by their own hydrogen bonds. • Forms alpha-helix ( spiral), beta sheets (like crinkled paper)

12. Secondary Structure • Alpha Helix (H-bonds in yellow) • Beta pleated sheets (parallel or antiparallel)

14. In the protein molecule there are zones with a bend. It is because of these bends that the helix and sheet sections fold onto the tertiary structure – the characteristic three-dimensional shape. Virtually, all water-soluble proteins, including blood proteins, enzymes, and antibodies, form a compact, roughly spherical globular shape as a result of this tertiary folding. A protein’s tertiary structure can be also filament – shaped. For example, collagen, the structural protein that makes up the fibrous component of skin, tendons, ligaments, cartilage, and bone - its build up of molecules shaped like thin cigars some 200 times as long as they are wide.

15. Tertiary Structure

16. Quaternary Structure • Some proteins have a fourth level of organization, called quaternary structure. These molecules are made up of two, three or more polypeptides, each folded into a secondary and tertiary shapes and then intertwined in a complex multichain unit. This kind of structure has a three – dimensional shape held together by week bonds. The hemoglobin molecule, which is composed of four hemo -bearing polypeptide chains, has the quaternary structure. • Not all proteins have this structure. When multiple polypeptide chains assemble to form one functional unit. Hemoglobin (4 chains), ATP Synthase, collagen (3 chains)

17. Biologists often classify proteins according to the functions they perform. Structural proteins, for example help to form bones, muscles , shells, leaves, roots, and even the microscopic cell ‘skeleton’ that provides shape and allow cell movement. Other examples are protein hormones, which serve as chemical messengers; antibodies, which fight infections; and transport proteins, which act as carriers of other substances (the hemoglobin protein in blood, for example transport oxygen). One of the most important kind of proteins in the enzymes, which change the speed (or catalyze) chemical reaction and thus underlie every biological activity.

18. 6.3 Section Summary 6.3 – pages 157-163 Proteins There are tens of thousands of different kinds of proteins; they have 5 main functions: • STRUCTURAL • STORAGE • TRANSPORT • DEFENSIVE • ENZYMES

19. Enzymes • Enzymes are the classic mediators of biological change, and change is central to life – change within atoms and molecules. Except in a few rare cases, the organism that is no longer changing is no longer living. • The study of enzymes began more than a century and a half ago. Since then, biologists have learned a great deal more about the roles of enzymes in living cells and about enzyme structure and function, including three unique characteristics. First, enzymes are specific. A given enzyme can act on only one type of compound or pair of reacting compounds, which is called its substrate. One enzyme can catalyze only one type of reaction. Second, the presence or absence of critical compounds can control enzymes. Third, at the end of the reaction enzymes are not changed they can act again and again with new substrates.

20. 6.3 Section Summary 6.3 – pages 157-163 Bio-molecule: Proteins • Enzymes are important proteins found in living things. An enzyme is a protein that changes the rate of a chemical reaction. Example: they speed the reactions in digestion of food. In living cells, enzymes serve as catalysts by reducing the activation energy necessary for biochemical reactions to take place.

21. Enzymes Enzymes act to bring substrates together or break them apart

22. Most enzymes are globular proteins, and the substrates on which they act often much smaller molecules than the enzymes themselves. Each protein enzyme has a unique three-dimensional shape arising from its primary, secondary, tertiary and (sometimes) quaternary structure. On the surface of each enzyme molecule there is one small area called the active site. The key to enzyme specificity is the shape of that site. The conformation of the active site complements the shape of the substrate (S) the enzyme acts on in much the same way that the key – hole of a lock fits around the key. It is this reciprocal matching of the three-dimensional shapes of active sites and substrates that accounts for enzyme specificity.

23. Enzymes function as catalysts by forming complexes with the reacting molecules. The first step in enzyme function is the formation of an enzyme –substrate complex. They change their own shapes slightly to improve the fit between enzyme and substrate. Such a change is called induced fit. The binding of substrates to an enzyme can increase the local concentration of the molecules, orienting the molecules correctly so than the reaction can take place most efficiently. All such changes act to lower the activation energy. Then they distort the shape of the substrate molecules slightly, as well, thereby helping them reach its transition state. Once substrate collides with and binds to an enzyme’s active site, the enzyme can perform its functions.

24. It distorts the bonds in the substrate molecule, and form the so called products from the substrate molecule, which can be released from the active site. The active site is unchanged and ready to catalyze a new reaction. • Three factors – temperature, concentration of enzymes, and concentration of substrates can affect the rates of enzyme-catalyzed reactions. If enzymes become saturated with substrate the reaction shows no further rate increase.

25. Because an enzyme’s activity depends on it precise three-dimensional shape, factors that affect its shape, can also affect, or even destroy, enzyme activity. One of the most important factors is the temperature. Enzymes intensity their activity up to 40°C. Over 60°C they stop their actions because the active site looses its three-dimensional structure. Most enzymes have a pH optimum or level of H+ concentration in which they function best. Cell and organisms have many mechanisms that help keep salt and H+ concentrations within narrow limits. There are factors which affect the three-dimensional shape of the active site and respectively can change enzyme’s activity. Some of them increase it – these are called activators. Others decrease enzyme’s activity – these are inhibitors.

26. Protein Folding in Sickle Cell Anemia