Proteins IUG, Fall 2012 Dr Tarek Zaida IUG, Fall 2012 Dr Tarek Zaida 1

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<ul><li> Slide 1 </li> <li> Proteins IUG, Fall 2012 Dr Tarek Zaida IUG, Fall 2012 Dr Tarek Zaida 1 </li> <li> Slide 2 </li> <li> 2 </li> <li> Slide 3 </li> <li> Amino Acids, Peptides, and Proteins Proteins are naturally occurring polymers composed of amino acid units joined one to another by amide (or peptide) bonds. Spider webs, animal hair and muscle, egg whites, and hemoglobin (the molecule that transports oxygen in the body to where it is needed) are all proteins. Proteins are naturally occurring polymers composed of amino acid units joined one to another by amide (or peptide) bonds. Spider webs, animal hair and muscle, egg whites, and hemoglobin (the molecule that transports oxygen in the body to where it is needed) are all proteins. 3 </li> <li> Slide 4 </li> <li> Peptides Are oligomers of amino acids that play important roles in many biological processes. For example, the peptide hormone insulin controls our blood sugar levels, Thus, proteins, peptides, and amino acids are essential to the structure, function, and reproduction of living organisms. Peptides Are oligomers of amino acids that play important roles in many biological processes. For example, the peptide hormone insulin controls our blood sugar levels, Thus, proteins, peptides, and amino acids are essential to the structure, function, and reproduction of living organisms. 4 </li> <li> Slide 5 </li> <li> Amino Acids The amino acids obtained from protein hydrolysis are -amino acids. That is, the amino group is on the -carbon atom, the one adjacent to the carboxyl group. The amino acids obtained from protein hydrolysis are -amino acids. That is, the amino group is on the -carbon atom, the one adjacent to the carboxyl group. 5 </li> <li> Slide 6 </li> <li> With the exception of glycine, where R is H, - amino acids have a stereogenic center at the -carbon. All except glycine are therefore optically active. They have the L configuration relative to glyceraldehyde. Note that the Fischer projection, used with carbohydrates, is also applied to amino acids With the exception of glycine, where R is H, - amino acids have a stereogenic center at the -carbon. All except glycine are therefore optically active. They have the L configuration relative to glyceraldehyde. Note that the Fischer projection, used with carbohydrates, is also applied to amino acids 6 </li> <li> Slide 7 </li> <li> The following table lists the 20 -amino acids commonly found in proteins. The amino acids are known by common names. Each also has a three-letter abbreviation based on this name, which is used when writing the formulas of peptides, and a one- letter abbreviation used to describe the amino acid sequence in a protein. The amino acids in the following table are grouped to emphasize structural similarities. The following table lists the 20 -amino acids commonly found in proteins. The amino acids are known by common names. Each also has a three-letter abbreviation based on this name, which is used when writing the formulas of peptides, and a one- letter abbreviation used to describe the amino acid sequence in a protein. The amino acids in the following table are grouped to emphasize structural similarities. 7 </li> <li> Slide 8 </li> <li> Of the 20 amino acids listed in the table, 12 can be synthesized in the body. The other 8, those with names shown in a blue color and referred to as essential amino acids, cannot be synthesized by adult humans and therefore must be included in the diet in the form of proteins. Of the 20 amino acids listed in the table, 12 can be synthesized in the body. The other 8, those with names shown in a blue color and referred to as essential amino acids, cannot be synthesized by adult humans and therefore must be included in the diet in the form of proteins. 8 </li> <li> Slide 9 </li> <li> 9 </li> <li> Slide 10 </li> <li> 10 </li> <li> Slide 11 </li> <li> The Amphoteric Nature of Amino Acids Amino acids are amphoteric. They can behave as acids and donate a proton to a strong base, or they can behave as bases and accept a proton from a strong acid. These behaviors are expressed in the following equilibria for an amino acid with one amino and one carboxyl group: Amino acids are amphoteric. They can behave as acids and donate a proton to a strong base, or they can behave as bases and accept a proton from a strong acid. These behaviors are expressed in the following equilibria for an amino acid with one amino and one carboxyl group: 11 </li> <li> Slide 12 </li> <li> 12 Zwitterion </li> <li> Slide 13 </li> <li> The isoelectric Point If placed in an electric field, the amino acid will therefore migrate toward the cathode (negative electrode) at low pH and toward the anode (positive electrode) at high pH. At some intermediate pH, called the isoelectric point (pI), the amino acid will have a net charge of zero. It will be unable to move toward either electrode. Each of the amino acids has a characteristic isoelectric points If placed in an electric field, the amino acid will therefore migrate toward the cathode (negative electrode) at low pH and toward the anode (positive electrode) at high pH. At some intermediate pH, called the isoelectric point (pI), the amino acid will have a net charge of zero. It will be unable to move toward either electrode. Each of the amino acids has a characteristic isoelectric points 13 </li> <li> Slide 14 </li> <li> 14 </li> <li> Slide 15 </li> <li> Essential &amp; Nonessential Amino Acids 15 </li> <li> Slide 16 </li> <li> Peptides Amino acids are linked in peptides and proteins by an amide bond between the carboxyl group of one amino acid and the - amino group of another amino acid. Emil Fischer, who first proposed this structure, called this amide bond a peptide bond. A molecule containing only two amino acids joined in this way is a dipeptide: Amino acids are linked in peptides and proteins by an amide bond between the carboxyl group of one amino acid and the - amino group of another amino acid. Emil Fischer, who first proposed this structure, called this amide bond a peptide bond. A molecule containing only two amino acids joined in this way is a dipeptide: 16 </li> <li> Slide 17 </li> <li> A dipeptide 17 </li> <li> Slide 18 </li> <li> 18 </li> <li> Slide 19 </li> <li> 19 Write out the abbreviated formulas for all possible tripeptide isomers of: 1. LeuAlaMet 2. GlyAlaSer Write out the abbreviated formulas for all possible tripeptide isomers of: 1. LeuAlaMet 2. GlyAlaSer </li> <li> Slide 20 </li> <li> A spiders Web 20 A spiders web is a device built by the spider to trap prey. Spider silk, a protein, is the main component of the web. Silk is composed largely of -s heets, a fundamental unit of protein structure. Many proteins have - sheets; silk is unique in being composed all most entirely of - sheets. </li> <li> Slide 21 </li> <li> Protein Three-Dimensional Structure composed of primary, secondary, and tertiary structures Functioning proteins are not simply long polymers of amino acids. These polymers fold to form discrete three- dimensional structures with specific biochemical functions. The amino acid sequence is called the primary structure. Three-dimensional structure resulting from a regular pattern of hydrogen bonds between the NH and the CO components of the amino acids in the polypeptide chain is called secondary structure. Functioning proteins are not simply long polymers of amino acids. These polymers fold to form discrete three- dimensional structures with specific biochemical functions. The amino acid sequence is called the primary structure. Three-dimensional structure resulting from a regular pattern of hydrogen bonds between the NH and the CO components of the amino acids in the polypeptide chain is called secondary structure. 21 </li> <li> Slide 22 </li> <li> The three-dimensional structure becomes more complex when the R groups of amino acids far apart in the primary structure bond with one another. This level of structure is called tertiary structure and is the highest level of structure that an individual polypeptide can attain. However, many proteins require more than one chain to function. Such proteins display quaternary structure, which can be as simple as a functional protein consisting of two identical polypeptide chains or as complex as one consisting of dozens of different poly- peptide chains. The three-dimensional structure becomes more complex when the R groups of amino acids far apart in the primary structure bond with one another. This level of structure is called tertiary structure and is the highest level of structure that an individual polypeptide can attain. However, many proteins require more than one chain to function. Such proteins display quaternary structure, which can be as simple as a functional protein consisting of two identical polypeptide chains or as complex as one consisting of dozens of different poly- peptide chains. 22 </li> <li> Slide 23 </li> <li> 1. The Primary Structure of Proteins The number and sequence of the amino acids in the protein chain. Primary structure is stabilized by peptide bonds. A slight change in the amino acid sequence (replacement of an amino acid with another), may change the entire protein. The number and sequence of the amino acids in the protein chain. Primary structure is stabilized by peptide bonds. A slight change in the amino acid sequence (replacement of an amino acid with another), may change the entire protein. 23 </li> <li> Slide 24 </li> <li> 2. Secondary Structure Polypeptide chains can fold into regular structures. Two types of secondary structure elements: 1. -helix 2. -sheet Polypeptide chains can fold into regular structures. Two types of secondary structure elements: 1. -helix 2. -sheet 24 </li> <li> Slide 25 </li> <li> 1. -helix Is a coiled structure stabilized by intrachain hydrogen bonds. Each turn of the helix contains a bout 3.6 amino acids. Hair &amp; wool are examples of protein with helical structure, both contain keratin. Is a coiled structure stabilized by intrachain hydrogen bonds. Each turn of the helix contains a bout 3.6 amino acids. Hair &amp; wool are examples of protein with helical structure, both contain keratin. 25 </li> <li> Slide 26 </li> <li> 26 (A)A ribbon depiction shows the carbon atoms and side chains (green). (B) A side view of a ball-and-stick version depicts the hydrogen bonds (dashed lines) between NH and CO groups. (C) An end view shows the coiled backbone as the inside of the helix and the side chains (green) projecting outward. (D) A space-filling view of part C shows the tightly packed interior core of the helix. (A)A ribbon depiction shows the carbon atoms and side chains (green). (B) A side view of a ball-and-stick version depicts the hydrogen bonds (dashed lines) between NH and CO groups. (C) An end view shows the coiled backbone as the inside of the helix and the side chains (green) projecting outward. (D) A space-filling view of part C shows the tightly packed interior core of the helix. </li> <li> Slide 27 </li> <li> -sheet Beta sheets are stabilized by hydrogen bonding between polypeptide strands instead of a single polypeptide strand, The - sheet is composed of two or more polypeptide chains called - strands. A - strand is almost fully extended rather than being tightly coiled as in the - helix. The distance between adjacent amino acids along a - strand is approximately 3.5 , in contrast with a distance of 1.5 along an - helix. The side chains of adjacent amino acids point in opposite directions. Beta sheets are stabilized by hydrogen bonding between polypeptide strands instead of a single polypeptide strand, The - sheet is composed of two or more polypeptide chains called - strands. A - strand is almost fully extended rather than being tightly coiled as in the - helix. The distance between adjacent amino acids along a - strand is approximately 3.5 , in contrast with a distance of 1.5 along an - helix. The side chains of adjacent amino acids point in opposite directions. 27 </li> <li> Slide 28 </li> <li> 28 The structure of a - strand. The side chains (green) are alternatively above and below the plane of the strand. The bar shows the distance between two residues Examples of proteins with -sheet are protein in silk (fibroin), and proteins that bind fatty acids </li> <li> Slide 29 </li> <li> Tertiary Structure The specific folding and bending of the coils into specific layers or fibers. This level of structure is the result of inter- actions between the R groups of the peptide chain. It is the tertiary structure that gives proteins their biological activity. Tertiary structure is stabilized by several types of bonds. The specific folding and bending of the coils into specific layers or fibers. This level of structure is the result of inter- actions between the R groups of the peptide chain. It is the tertiary structure that gives proteins their biological activity. Tertiary structure is stabilized by several types of bonds. 29 </li> <li> Slide 30 </li> <li> Types of Bonds that stabilize tertiary structure 1.Hydrogen bonds 2.Disulfide bridges 3.Hydrophobic interactions 4.Salt bridges between positively &amp; negatively charged groups within the protein. 5.Nonpolar amino acids are folded on the inside of the protein, and polar amino acids are on the outside where they react with water to form polar group interactions. 1.Hydrogen bonds 2.Disulfide bridges 3.Hydrophobic interactions 4.Salt bridges between positively &amp; negatively charged groups within the protein. 5.Nonpolar amino acids are folded on the inside of the protein, and polar amino acids are on the outside where they react with water to form polar group interactions. 30 </li> <li> Slide 31 </li> <li> Quaternary Structure It occurs when a protein has at least 2 units combine together to form a complex. 31 </li> <li> Slide 32 </li> <li> The 2 2 tetramer of human hemoglobin. The 2 2 tetramer of human hemoglobin. 32 </li> <li> Slide 33 </li> <li> Percent Composition Average percentage of nitrogen in protein is 16%. 16% Nitrogen = 1/6 of protein content. Protein is the major food containing nitrogen. Chemists can determine the amount of protein present in food substance by deter- mining the amount of nitrogen present. Calculation of protein in food can be done by multiplying the weight of nitrogen by 6 and converting it to a percentage of the total. Average percentage of nitrogen in protein is 16%. 16% Nitrogen = 1/6 of protein content. Protein is the major food containing nitrogen. Chemists can determine the amount of protein present in food substance by deter- mining the amount of nitrogen present. Calculation of protein in food can be done by multiplying the weight of nitrogen by 6 and converting it to a percentage of the total. 33 </li> <li> Slide 34 </li> <li> % protein in food = grams of Nitrogen x 6 Example: If 100 g of food yield 4 g of nitrogen on chemical analysis. Calculate the % protein in the sample? Since the amount of nitrogen in protein is 1/6 of the total amount...</li></ul>