Chapter 1 structures and functions of proteins

1. Chapter 1 structures and functions of proteins

2. contents • 1.chemical components • 2.molecular structures • 3.biological functions • 4.structure-function relationship • 5.physical and chemical properties • 6.exploration of proteins • 7.protemics: a new frontier

3. What are proteins? • Proteins are macromolecules composed of amino acids linked together through peptide bonds.

4. How are about proteins? • The most widely distributed biomolecules • The most abundant biomolecules(45% of human body) • The most complex biomolecules • The most diversified biological functions

5. What are the many biological functions of proteins? • Enzymes: catalysts that accelerate the rates of biological reactions • Regulatory proteins: control metabolism and gene expression • Transport proteins: carry substances from one place to another • Storage proteins: reservoirs of amino acids or other nutrients • Contractile and motile proteins: movement • Many proteins: structural role • Proteins: signaling pathways • Proteins: protective and exploitive functions • Few proteins: exotic functions

6. What do proteins do? • Proteins are a diverse and abundant class of biomolecules, constituting more than 50% of the dry weight of cells. • Composition: 20 kinds of amino acids linked in series • Polymers composed of hundreds or even thousands of amino acids

7. Simple proteins (only contain amino acids) proteins Conjugated proteins (contain various chemical constituents, nonprotein part) Do proteins have chemical groups other than amino acids? • Glycoproteins: containing carbohydrate groups • Lipoproteins: associated with lipid molecules • Nucleoproteins: joined with nucleic acids • Phosphoproteins: contain phosphate groups • Metalloproteins: protein-metal complexes • Hemoproteins: contain heme • Flavoproteins: contain riboflavin Prosthetic group

8. Chemical components of proteins • Major elements • C (carbon) (50-55%),H (hydrogen)(-7%), • O (oxygen)(19-20%),N (nitrogen)(13-19%), • S (sulfur) (-4%) • Trace elements • P (phosphorus), Fe (iron), Cu (copper), • Zn ( zinc), I (iodine),……

9. The average nitrogen content in proteins is about 16%, and proteins are the major source of N in biological systems. • Protein can be quantified by testing the quantity of nitrogen: • 1 gram of nitrogen equals to 6.25 gram of protein • Protein in 100g sample=N per gram x6.25x100

10. Amino acids • The basic building blocks of proteins • About 300 types of AAs in nature, but only 20 types are used for protein synthesis in biological systems. (from bacteria to human) • A amino group, a carboxyl group, a H atom and a R group are connected to a C atom. • The C atom is an optically active center.

11. A carbon atom bearing four different substituents is said to be chiral Asymmetric or chiral carbon

12. The two enantiomers of each amino acid defined by the a-carbon are designated D- and L- forms (D for Dextrorotatory, L for Levorotatory)

13. The D- and L-forms of amino acids are named in reference to the absolute configuration of D- and L- glyceraldehydes.

14. L-Amino Acids Since all amino Acids but glycine are chiral molecules, it’s possible to have enantiomers. However, nature uses only one enantiomer, the L-amino acid. L-glyceraldehyde (an L-sugar) L-serine (an L-amino acid) All of the amino acids derived from natural proteins are of the L-configuration.

15. Amino acids are organic acids containing an amino group. They are the basic units of a protein. The most common amino acids are the L-α-amino acids. • Common structure • Classification • Properties

16. α 1. Common structure • 20 L-α- Amino Acids Each has a carboxyl group and an amino group bonded to the same carbon atom, designated as the α-carbon Each has a different side chain (or R group, R=“Remainder of the molecule”).

17. Amino acid structure Different side-chain (R group) Different chemical and physical properties Amino group Carboxylic acid group

18. In protein chemistry, we use Greek letter nomenclature Starting from the carboxyl group, and naming the rest carbon atoms sequentially

19. classification • Two methods • 1.According to the structures of R groups • 2. According to the polarities of R groups • The R groups, also called side chains, make • each AA unique and distinctive. • R groups are different in their size, charge, • hydrogen bonding capability and chemical • reactivity.

20. Grouped as: • 1. Neutral(Nonpolar )or hydrophobic amino acids • Glycine, Leucine, Isoleucine, Alanine, Phenylalanine, Proline, Valine, Methionine, Tryptophan • R groups are non-polar, hydrophobic aliphatic • or aromatic groups. • R groups are uncharged. • AAs are insoluble in H2O

21. 2. Neutral (uncharged) polar amino acids • Serine, Threonine, Cysteine, • Tyrosine, Asparagine, Glutamine • R groups are polar: -OH, SH, and –NH2. • R groups are highly reactive • AAs are soluble in H2O, that is hydrophilic

22. 3. Acidic amino acids: Aspartic acid, • Glutamic acid • R groups have –COOH. • R groups are negatively charged at physiological • pH(=7.4) • AAs are soluble in H2O • 4. Basic amino acids : Lysine, • Arginine • Histidine • R groups have one –NH2 • R groups are positively charged at neutral pH(=7.0) • AAs are highly hydrophilic

23. 20 Common Amino Acids • You should know names, structures, 3-letter and 1-letter symbols

24. Amino Acid Classification • Aliphatic • Aromatic • Sulfur containing • Polar/uncharged • basic/acidic Hydrophobic- water fearing. non-polar side chains Hydrophilic- water loving. polar, neutral chains negatively charged, positively charged

25. CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ Methyl Isopropyl Isobutyl Sec-butyl Phosphorylation

26. CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+

27. CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ CH COO- NH3+ Benzene + N COO- H2 Guanidino Imidazole Indole

28. Abbreviations for 20 amino acids • Nonpolar or hydrophobic amino acids: • Leucine (Leu, L), Isoleucine (ILe, I), Alanine (Ala, A), • Phenylalanine (Phe, F), Proline (Pro, P), Valine (Val , V), • Methionine (Met, M), Tryptophan (Try, W) ,Glycine (Gly, G) • Neutral (uncharged) polar amino acids: • Serine (Ser, S), Threonine (Thr, T), • Cysteine (Cys, C), Tyrosine (Tyr, Y), • Asparagine (Asn, N), Glutamine (Gln, Q) • Acidic amino acids: • Aspartic acid (Asp, D), Glutamic acid (Glu, E) • Basic amino acids: • Lysine (Lys, K), Arginine (Arg, R), Histidine (His, H)

29. ProlineImino acid Special amino acids: Pro has an imino group, instead of an amino group, forming a five-membered ring structure, being rigid in conformation.

30. According to the structures of R groups • With aliphatic side chains: Gly Ala Val Leu Ile • With side chains containing hydroxylic (OH)groups: Ser Thr Tyr • With side chains containing sulfur atoms: Cys Met • With side chains containing acidic groups or their amides: Asp Asn Glu Gln • With side chains containing basic groups:Lys Arg His • Containing aromatic rings: Phe Tyr Trp • Imino acids: Pro

31. Essential Amino Acids All 20a-amino acids we will study are required for protein synthesis, but the human body is able to synthesize only 12 of them. The other 8 (the essential amino acids) must be obtained from food. The essential amino acids includethreonine, isoleucine, phenylalanine, methionine, tryptophan, valine, leucine, and lysine. -Tip MTV Hall

32. Disulfide bond -SH (thiol) group of two Cys in proteins can be oxidized to form a covalent disulfide bond

33. gly • Optically inactive

34. Uncommon amino acids Collagen: Hydroxylysine Hydroxyproline

35. Phosphorylated amino acids - signal transduction Ser Thr Tyr

36. Properties of Amino Acids • capacity to polymerize • chirality • novel acid-base properties • varied structure and chemical functionality • Dissociation and pI

37. Zwitterions A Zwitterion is a dipolar ion. Since amino acids contain both an acid and a base, an internal acid-base reaction forms a zwitterion. amino acid zwitterion Amino acids exist primarily as zwitterions.

39. Zwitterions Amino acid zwitterions are amphoteric. They can react as either acids or bases. In acid solution zwitterion protonated In base solution zwitterion deprotonated

40. Isoelectric Points The isoelectric point of an amino acid occurs at the pH where the amino acid exists as the zwitterion. protonated acid solution low pH zwitterion isoelectric point deprotonated base solution high pH Cation amphoteric anion PI is determined by pK, the ionization(dissociation) constant of the ionizable groups

41. Titration Curve for Alanine pK1 carboxylic acid = 2 pK2 amino group = 10 pI = (pK1+ pK2)/2 pI (isoelectric point) = the pH at which the number of positive and negative charges on a population of molecules is equal (i.e. no net charge).

42. Titration Curve for Glutamic Acid pK1 carboxylic acid = 2.2 pK2 R group = 4.3 pK3 amino group = 9.7 pI = (pK1+ pK2)/2 pI = (2.2+4.3)/2 pI = 3.25

43. Titration Curve for Lysine pK1 carboxylic acid = 2.2 pK2 amino group = 9.0 pK3 R group = 10.5 pI = (pK2+ pK3)/2 pI = (9+10.5)/2 pI = 9.75

44. There is a specific pH (namedpI)at which an amino acid has equal positive and negative charge. An amino acid does not move in an electric field at its pI. Isoelectric point The amino acids are positively charged at pH smaller than their pI values, negatively charged at pH larger than their pI values.

45. Isoelectric point • No net charge • Minimum solubility in water • protein will precipitate out at its isoelectric point • can separate amino acids and peptides in electrophoresis: • + (cation)charged amino acids move to – electrode (anion) • - charged amino acids move to + electrode • amino acids at their isoelectric points do not move

46. Electrophoresis A mixture of histidine, serine, and glutamic acid can be separated by electrophoresis at pH = 5.68. - + positively charged (protonated) histidine negatively charged (deprotonated) glutamic acid serine at its isoelectric point at pH = 5.68

47. UV-absorbing Properties of Amino Acids Spectroscopic methods: measure the absorption and emission of energy of different frequencies by molecules and atoms. Absorption peak: 280nm detection of the protein • Only three amino acids, Phe, Tyr, and Trp, absorb light in the near UV range (230 nm-300 nm). These amino acids dominate the UV absorption spectra of proteins. The wavelength maxima for tyrosine and tryptophan are around 280 nm. In contrast, nucleic acids (we will discuss later) have absorption maximum of 260 nm. Thus a simple UV scan can allow one to distinguish between protein and nucleic acids.

48. Functional signficance of AA R-groups In solution it is the nature of the amino acid R-groups that dictate structure-function relationships of peptides and proteins. The hydrophobic amino acids will generally be encountered in the interior of proteins shielded from direct contact with water. Conversely, the hydrophilic amino acids are generally found on the exterior of proteins as well as in the active centers of enzymatically active proteins. The imidazole ring of histidine allows it to act as either a proton donor or acceptor at physiological pH. Hence, it is frequently found in the reactive center of enzymes. The thiol of cysteine is able to form a disulfide bond with other cysteines: Cysteine-SH + HS-Cysteine <--------> Cysteine-S-S-Cysteine Called Cystine Disulfide bonding between cysteines in different polypeptide chains of oligomeric proteins plays a crucial role in ordering the structure of complex proteins, e.g. the insulin receptor.

49. Key points: • 20 amino acids: structure and classification • Acid-base properties amino acids and pI • Optical and Stereochemical Properties

50. Molecular structures of proteinLinkage between amino acids-----Peptide and peptide bond Peptides are polymers of amino acids linked by peptide bonds. • A peptide bond is a covalent bond formed between the carboxyl group of one AA and the amino group of its next AA with the elimination of one H2O. Peptide bond formation involves removal of 1 mol of water between the α-carboxyl group of one amino acid and the α-amino group of another amino acid.