1. 1 2- Proteins Many Structures, Many Functions 1.A polypeptide is a polymer of amino acids connected in a specific sequence 2.A protein’s function depends on its specific conformation

2. 2  Their functions include structural support, storage, transport of other substances, intercellular signaling الإشارات بين الخلوية, movement, and defense against microbes.  Some proteins works as enzymes in the cell that regulate metabolism الأيض by accelerating تسريع chemical reactions.  Humans have tens of thousands of different proteins, each with their own structure and function.  All protein polymers are constructed from تتركب من the same set of 20 monomers, called amino acids.  Polymers of proteins are called polypeptides ببتيدات عديدة.  A protein consists of one or more polypeptides folded and coiled into a specific conformation 2-Proteins

3. 3 - The physical and chemical characteristics صفات of the R group determine the unique characteristics of a particular amino acid. - The physical and chemical characteristics صفات of the R group determine تحدد the unique characteristics of a particular amino acid. Side chain Amino group Carboxyl group - They are Polymers of amino acids (constructed from 20 amino acids) (to form Polypeptides). General Formula of the Amino Acid: CHR N H H C OHOHOHOH O R - The side chain R links with ترتبط بـ different compounds - These components include a hydrogen atom, a carboxyl group, an amino group, and a variable متغيرة R group (or side chain). - Differences in R groups produce the 20 different amino acids.

4. 4 1.Hydrophobic: the amino acids that have hydrophobic R groups (non-polar). Fig. 5.15, Page 72 Amino acids الأحماض الأمينية 2- Hydrophilic: the amino acids that have polar R groups, making them hydrophilic. 3- Ionized: the amino acids with functional groups that are charged (ionized) at cellular pH (7). So, some R groups are bases, others are acids. 3- Ionized: the amino acids with functional groups that are charged (ionized) at cellular pH (7). So, some R groups are bases, others are acids.

5. 5 1.Hydrophobic: the amino acids that have hydrophobic R groups (non-polar). Fig. 5.15, Page 72 Amino acids

6. 6 2- Hydrophilic: the amino acids that have polar R groups, making them hydrophilic. 3- Ionized: the amino acids with functional groups that are charged (ionized) at cellular pH (7). So, some R groups are bases, others are acids. 3- Ionized: the amino acids with functional groups that are charged (ionized) at cellular pH (7). So, some R groups are bases, others are acids. Fig. 5.15, Page 73

7. 7 Peptide bonds Peptide bond formed between the carboxyl group of one amino acid and the amino group of the other by dehydration. OHOHOHOH C C H R N H H O H CHR NHC OHOHOHOH O Peptide bond Peptide Page 73, Fig. 5.16 Polypeptide (Protein)Dehydration

8. 8 Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a peptide bond.Amino acids are joined together when a dehydration reaction removes a hydroxyl group from the carboxyl end of one amino acid and a hydrogen from the amino group of another. The resulting covalent bond is called a peptide bond. Fig. 5.16, Page 73 Repeating the process over and over عدة مرات creates a long polypeptide chain.Repeating the process over and over عدة مرات creates a long polypeptide chain. –At one end is an amino acid with a free amino group the (the N-terminus) and at the other is an amino acid with a free carboxyl group the (the C- terminus). The repeated sequence (N-C-C) is the polypeptide backbone.The repeated sequence (N-C-C) is the polypeptide backbone. Attached to the backbone are the various R groups.Attached to the backbone are the various R groups. Polypeptides range in size from a few monomers to thousands.Polypeptides range in size from a few monomers to thousands.

9. 9 The folding إلتفاف of a protein from a chain of amino acids occurs spontaneously ذاتيا.The folding إلتفاف of a protein from a chain of amino acids occurs spontaneously ذاتيا. There are three levels of structure: primary أولى, secondary ثانوى, and tertiary ثلاثى structure, are used to organize the folding within a single polypeptide.There are three levels of structure: primary أولى, secondary ثانوى, and tertiary ثلاثى structure, are used to organize the folding within a single polypeptide. Quaternary رباعى structure arises when two or more polypeptides join to form a protein.Quaternary رباعى structure arises when two or more polypeptides join to form a protein. Levels of Protein Structure

10. 10 1.Primary structure: It is a single polypeptide chain of amino acids. –Lysozyme, an enzyme that attacks bacteria, consists of a polypeptide chain of 129 amino acids. –A slight change تغيير طفيف in the primary structure can affect a protein’s conformation and ability to function. Fig. 5.18, Page 75

11. 11 Sickle cell disease المنجلية:Sickle cell disease المنجلية: an abnormal hemoglobin because of a single amino acid substitution تغيير. an abnormal hemoglobin because of a single amino acid substitution تغيير. –These abnormal hemoglobins crystallize, deforming يُكسر the red blood cells and leading to clogs إنسداد in tiny blood vessels. Fig. 5.19, Page 75

12. 12 2- The secondary structure: Results from hydrogen bonds at regular intervals على أبعاد متساوية along the polypeptide backbone. A. Coils A. Coils الحلزونى (α helix ) are typical shapes that develop from secondary structure B.Folds B.Folds ( β pleated sheets ) الشيت المُجعد. Composed of several parallel αhelix coils attached by H bonds Fig. 5.20, Page 76

13. 13 An example for folds (beta pleated sheets) الشيت المُجعد: Is the structural properties of silk because of the presence of so many hydrogen bonds makes each silk fiber stronger than steel. Fig. 5.21, Page 77

14. 14 Tertiary structure:Tertiary structure: among خلال R groups between R groups and the polypeptide backbone is determined by a variety of interactions among خلال R groups and between R groups and the polypeptide backbone. hydrogen bonds ionic bonds Van der Waals interactions –These interactions include hydrogen bonds among polar areas, ionic bonds between charged R groups, and hydrophobic interactions and Van der Waals interactions among hydrophobic R groups. Fig. 5.22, Page 77 disulfide bridgesWhile these three interactions are relatively weak, disulfide bridges, strong covalent bonds that form between the sulfhydryl groups (SH) of cysteine monomers, stabilize the structure.

15. 15 4- The quaternary structure: Results from the aggregation تجمع of two or more polypeptide chains. A.Collagen A.Collagen is a fibrous protein of three polypeptides that are supercoiled, and function in connective tissues. A.Hemoglobin A.Hemoglobin is a globular protein with two copies of two kinds of polypeptides (2α and 2β). Fig. 5.23, Page 78 Collagen Hemoglobin

16. 16 Fig. 5.24, Page 79 The 4 forms of protein

17. 17 It is the change of protein’s conformation in response to إستجابة لـ the physical and chemical conditions. denatureFor example, alterations تغيير in pH, salt concentration, temperature, or other factors can denature يفرد a protein. –These forces break the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein’s complicated shape. Some proteins can return to their original shape again after denaturation, but others cannot. Denaturation of protein فرد البروتين

18. 18 Fig. 5.25, Page 79 مفرود Denaturation of protein فرد البروتين فرد إعادة إلى طبيعته

19. 19 Amino acids Primary structure Secondary structure Tertiary structure Quaternary structure 1- Hydrophobic Interaction (Van der Waals interaction); 2- H bonds; 3- Ionic bonds; 4- Di-sulfide bridges; Single chain of amino acids e.g. Lysozyme Coils & Folds H bonds e.g. silk e.g. Collagen & Hemoglobin two or more polypeptidechains PeptidesPeptides Peptide ponds Dehydration Hydrophobic () Hydrophobic (non-polar R group) Hydrophilic () Hydrophilic (polar R group) Ionized (charged functional groups Ionized (charged functional groups) ProteinsProteins Polypeptides