Amino Acids and Proteins Hamad Ali Yaseen, PhD MLS Department, FAHS, HSC, KU Biochemistry 210 Chapter 22

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1 Amino Acids and Proteins Hamad Ali Yaseen, PhD MLS Department, FAHS, HSC, KU Biochemistry 210 Chapter 22 Importance of Proteins Main catalysts in biochemistry: enzymes (involved in virtually every biochemical reaction) Structural components of cells (both inside and outside of cells in tissues) Regulatory functions (if/when a cell divides, which genes are expressed, etc.) Carrier and transport functions (ions, small molecules) 1

2 Protein Function and Structure Protein function depends on both amino acid content, and amino acid sequence. Protein fold into diverse shapes such as spherical elipsoidal long strands, etc. All information for 3-D structure is contained in the linear sequence of amino acids. Levels of Protein Structure Primary Structure - amino acid sequence in a polypeptide Secondary Structure - local spatial arrangement of a polypeptide s backbone atoms (without regard to side chain conformation) Tertiary Structure - three-dimensional structure of entire polypeptide Quaternary Structure - spatial arrangement of subunits of proteins composed of multiple polypeptides (protein complexes) 2

3 Amino Acids Proteins are chains of Amino Acids To understand protein function, we must first understand the nature of amino acids. An Amino Acid is an organic compound containing an amino group and a carboxyl group. 3

4 20 Common Amino Acids You should know names, structures, 3-letter and 1-letter codes Non-polar amino acids Polar, uncharged amino acids Acidic amino acids Basic amino acids Amino Acids We can synthesize many thousands amino acids but nature is more restrictive and uses 20 common amino acids to make the proteins. 4

5 Amino Acids Building Blocks of Proteins All but one amino acid of the 20 fit into the formula Amino Acids Amino acids are essentially α-amino acids: alpha carbon (IUPAC #2 position) H 2 N C COOH R 5

6 Amino Acid The Amino Acid that doesn t fit into the formula is (Proline). It differs only in that it has a bond between R and N. The 20 amino acids are called alpha amino acids The 20 Amino Acids Found in Proteins 6

7 Amino Acids The properties of Amino Acids are determined by the R group. Among these aspects is polarity. So Amino acids can be classified into: Non Polar Polar Uncharged Acidic Basic Note that non polar side chains are hydrophobic (they repel water) The rest are hydrophilic. 7

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9 Amino Acids All Amino Acids (except Glycine where R is H) are chiral with (carbon) stereocenters. Each amino acid with one stereocenter exists in two forms (enantiomers). Nature mainly makes the L-isomer. 9

10 Stereoisomers of -amino acids All amino acids in proteins are L-amino acids, except for glycine, which is achiral. RS Nomenclature System (Cahn, Ingold, Prelog System) 10

11 What are Zwitterions? Carboxylic acids, RCOOH, cannot exist in the presence of a moderately weak base such as NH3. So they donate a proton to become carboxylate ions RCOO -. Likewise, amines RNH2, cannot exist in the presence of a moderately weak acid such as acetic acid so they Gain a proton to become substituted ammonium ion RNH3 +. In water solution, the -COOH donates a proton to the NH2 so that an amino acid actually has the structure : Structure of -amino acids 11

12 What are Zwitterions? Compounds that have a positive charge on one atom and a negative charge on the other are called Zwitterions. Zwitter in German means hybrid. Amino acids are Zwitterions in water solutions and solid states. Zwitterions and Amino acid properties Being Zwitterions explains their physical properties. All of them are solids with high melting points. 12

13 Even though both acids and amines are present in the same molecule, they mostly behave as though they were separate entities: 25 Summary: At low ph, proton concentration [H+]is high. Therefore, both amines and carboxylic acids are protonated. (- NH 3+ & -COOH) At high ph, proton concentration is low. Therefore, both amines and carboxylic acids are deprotonated. (- NH 2 & -COO - ) At neutral ph, amines are protonated(-nh 3+ ) and carboxylates are deprotonated(-coo - ) The PH at which all he molecules have equal positive and negative charges is called Isoelectric point (pi) 13

14 Acid-Base Properties of Amino Acids Draw the following chemical structures for glycine: (Non-existent form:) H 2 N CH 2 - COOH ph=1: ph=7: ph=12: Acid-Base Properties of Amino Acids Draw the following chemical structures for glycine: (Non-existent form:) H 2 N CH 2 - COOH ph=1: + H 3 N CH 2 - COOH ph=7: ph=12: 14

15 Acid-Base Properties of Amino Acids Draw the following chemical structures for glycine: (Non-existent form:) H 2 N CH 2 - COOH ph=1: + H 3 N CH 2 - COOH ph=7: + H 3 N CH 2 COO - ph=12: Acid-Base Properties of Amino Acids Draw the following chemical structures for glycine: (Non-existent form:) H 2 N CH 2 - COOH ph=1: + H 3 N CH 2 - COOH ph=7: + H 3 N CH 2 COO - ph=12: H 2 N CH 2 COO - 15

16 Low ph Neutral ph High ph Formation of a Peptide 16

17 Amino acids are polymerized via peptide bonds: Definition: Amino acid polymers of 50 amino acids are called polypeptides, peptides, oligopeptides, etc. Amino acids polymer of >50 amino acids are called proteins. 17

18 Peptide The order of amino acids in the peptide chain plays a role in determining the functionality of the peptide. Dipeptide 18

19 Cross links between peptide chains: Disulfide linkages between individual cysteines are called cystines: Insulin is the smallest protein, with 51 amino acids in two chains linked by cystine (disulfide) cross links: 19

20 Questions If I give you a peptide chain. You need to know how to identify peptide bonds. If I give you structures of three amino acids. You need to know how to form peptide chain. Proteins Amino acids polymer of >50 amino acids are called proteins. Properties of proteins are based on properties of the peptide backbone and properties of side chains. The backbone is the N-C-C-N-C-C- and so on. 20

21 Levels of Protein Structure Primary (1 ) Protein Structure linear sequence of amino acids. Secondary (2 ) Protein Structure localized regional structures Tertiary (3 ) Protein Structure overall shape of proteins Quaternary (4 ) Protein Structure interactions between proteins Protein Structure: Twisting about various bonds in the polypeptide backbone gives proteins a variety of shapes. Bond angles give rise to secondary structures. Then, localized secondary structures help drive the peptide folding that gives rise to tertiary structure. 21

22 Primary Structure It consists of the sequence of amino acids that makes up the chain. The order of Amino Acids is important. Secondary Structure Proteins can fold or align themselves in such a manner. These patterns are called secondary structures. Alpha helix Beta sheet 22

23 Protein Structure Secondary Structure in Proteins: Pauling and Corey proposed two secondary structures in proteins many years before they were actually proven: alpha helix beta - sheet Both of these secondary protein structures are stabilized by hydrogen bonding between the carbonyl oxygen atoms and the nitrogen atoms of amino acids in the protein chain. The alpha (α) helix: 23

24 beta sheet (antiparallel): beta sheet (artistic representations): 24

25 Examples of beta-sheet domains in proteins: Tertiary Structure (page 598) It is the 3D arrangement of every atom in the molecule. Unlike, Secondary structure it includes the interactions of side chains. And not just the backbone. It is Stabilized by: Covalent bonds. For example Disulfide bonds. Hydrogen bonds. Between side chains or side chain and backbone. Salt Bridges: this occurs between two amino acids with ionized side chains. Hydrophobic interaction: Metal ion coordination. 25

26 Tertiary (3 ) Structure of Protein Water-soluble proteins fold into compact structures with nonpolar cores. Tertiary (3 ) Structure the Protein Myoglobin Water-soluble proteins fold into compact structures with non-polar cores. 26

27 In the case of myoglobin and many other proteins, the majority of hydrophobic amino acids (yellow) are found inside in structure: Quaternary Structure The highest level of protein organization. Applies for proteins with more than peptide chain. 27

28 The Cro protein of Lambda bacteriophage is a dimer of identical subunits: Hemoglobin is a protein tetramer, containing two identical pairs of subunits: 28