Section 14.5 Uncommon amino a cids

1. Uncommon amino acids, amino acids forming proteins, and primary structure of a proteinSections 14.5-14.8By Melissa Myers, Caroline Stepanik, and Jade Coxe

2. Section 14.5 Uncommon amino acids • Along with the 20 amino acids found in proteins there are many other amino acids known • Normally produced after one of the standard amino acids has joined with a protein • Occur in some but not all proteins • Uncommon amino acids are made from common amino acids by the modification of the parent amino acid after the protein is synthesized by the organism • This process is called Post-Translational Modification

3. Uncommon Amino Acids Cont. • Hydroxyproline and hydroxylsine are found in a few connective tissue proteins like collagen • Hydroxyproline and hydroxylsine are different from their parent amino acids because they have hydroxyl groups on their side chains

4. 14.6 How do amino acids combine to form proteins? • Each amino acid has a carboxyl group and an amino group

5. Amino Acids combining to form protein • Takes place in cells by a mechanism • Product is an amide • 2 amino groups join by peptide bond • Product is a dipeptide

6. Amino acids combining to form proteins cont. • Glycine and alanine can also be combined to form alanylglycine • Forms different dipeptides • The 2 dipeptides are isomers • Each compound is different and contains different properties • The order of the amino acids is important to its structure and function

7. Amino Acids Combining to Form Proteins cont. • Any 2 amino acids can be combined to form dipeptides • Each dipeptide contains a –COO⁻ and -NH₃ • A third amino acid can be added to get a tripeptide • A chain can have 100s and 1,000s of amino acids • Short chains are peptides • Longer chains are polypeptides; and even longer chains are proteins

8. Amino Acids Combining to Form Proteins cont. • Polypeptides and proteins are used interchangeably • Polypeptide chain (30-50 amino acids) • Amino acids in a chain are called residues • 1 or 3 letter abbreviations are used to represent peptides and proteins • Ex: alanylglycyllysine: AGK or Ala-Gly-Lys

9. Amino Acids Combining to Form Proteins cont. • C-terminal : the residue with the free -COO⁻ group • N-terminal : the residue with the –NH₃ group • N-terminal is usually written on the left • Proteins are synthesized from N-terminus → C-terminus

10. Section 14.7 Properties of Proteins • Continuing pattern of peptide bonds form the backbone of the protein • R groups are called side chains • 20 different amino acid side chains give variety and determine the physical and chemical properties of proteins • Acid base behavior is one of the most important properties

11. Properties of Proteins cont. • Proteins behave as zwitterions • The side chains of Glutamic and aspartic acid provide acidic groups • Lysine and arginine provide basic groups • Isoelectric point of proteins occur at the pH in which there is an equal negative and positive charge

12. Properties of Proteins Cont. • Any pH above the isoelectric point means the protein molecules have a negative charge • Proteins act as buffers in the blood • The water solubility of proteins often depends on the repulsive charges between like charges on their surface • When the molecules are at a pH level in which they have a net positive or net negative charge the presence of the charges makes the protein molecules repel

13. Properties of Proteins cont. • Repulsive forces are the smallest at the isoelectric point when the net charges are zero • When there is no repulsive force the molecules clump together and become less soluble • Proteins are least soluble in water at their isoelectric points and can become precipitated from their solutions

14. Properties of Proteins cont. • Primary structure describes the linear organization of the amino acids in the polypeptide chain • Secondary structure refers to the repeating patterns like the helix conformation • Tertiary structure explains the overall conformation of the polypeptide chain • Quaternary structure applies to proteins containing more than one polypeptide chain and how the chains are spatially related

15. Properties of Proteins

16. Section 14.8 Primary Structure of Proteins • The sequence of amino acids is a protein • The larger number of peptide and protein molecules have different sequences of amino acids • These structures allow proteins to perform its functions

17. Structures of Proteins • To figure out how many different proteins come from different sequences of 20 amino acids take 20 to the nth power. • There are 20 possibilities for N-terminal amino acid and 20 possibilities for the C-terminal amino acid • Ex. Dipeptide 20 x 20 = 400 or 20^2 = 400 different dipeptides possible

18. Tripeptides • 20 x 20 x 20 = 8000 different tripeptides possible • The number of proteins that can be made with a small protein with 60 amino acid residues would be 20^60 = 10^78 • Each peptide or protein has its own unique sequence of amino acids • The assignment of positions of the amino acids in the sequence starts at the N-terminal end

19. Structures of Proteins • Proteins can have secondary, tertiary, and sometimes quaternary structures • The primary structure of a protein determines to a large extent of the most frequently occurring secondary and tertiary ones. • The chain is able to fold and curve due to the sequence of the amino acids in the chain ( without its 3 dimensional shape it cannot function properly)

20. Structures of Proteins • Changing the order of amino acids in a chain may or may not affect the function of the protein • Ex. 1. Hormone insulin • Human insulin: 2 chains with 51 amino acids (insulin is needed for utilization of carbohydrates) it is also needed for people who have diabetes and must take insulin projections; the amount of human insulin is too small, so bovine insulin (cattle, hogs, or sheep) is used instead. The differences are at the positions of 8, 9, and 10 of chain A & C-terminal 30 of the B chain.

21. Structures of Proteins • To produce human insulin from bacteria, DNA techniques are being used • Also with insulin some patients can be allergic to the bovine insulin due to the substituting of an amino acid, but may use insulin of sheep and hogs and not have a reaction.

22. Structures of Proteins • Ex.2. Hemoglobin • Making one change to an amino acid can be enough to cause a fatal disease (chain of 146) and the disease is called sickle cell anemia. • There are cases where the sequence does not have an effect on the function, but most of the time the sequence of amino acids is very important

23. THE END!