Shu-Ping Lin, Ph.D.

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1 Amino Acids & Proteins Shu-Ping Lin, Ph.D. Institute te of Biomedical Engineering ing Website: edu tw/pweb/users/splin/ Date:

2 Amino Acids Proteins are the basis for the major structural components of animal and human tissue Linear chains of amino acids residues Amino Acids (AA): 1 central carbon atom + 4 subgroups {amino group ( NH 2 ), carboxyl group ( COOH), hydrogen atom, and a distinctive side chain (R)} Organic molecules serve as chemical messengers between cells or function as important intermediates in metabolic processes. Different R groups Different properties and AA Mirror-image forms (stereoisomers) L and D-isomers Only L-amino acids are in proteins, D-amino acids are widely in bacterial cell walls. 300 AA in nature, but only 20 of these in proteins Not every protein contains all of the 20 AA types. All proteins have an AA containing sulfur Make peptides and Proteins

3 Synthesis of Polypeptides & Proteins Amino group join to carboxyl group and lose one water molecule Condensation reaction (amide synthesis reaction) Covalent bond between 2 amino acid residues is called a peptide bond or amide bond Form backbone of the polypeptides and expose side chains R Result in proteins with intricate 3D structures and a remarkable range of functions Polypeptides: linear polymers, a head-to-tail fashion, a sense of direction grow from amino group toward carboxyl group (Amine end (N terminal) is always on the left, while the acid end (C terminal) is on the right. First/Start amino acids in most polypeptides is the sulfur-containing amino acid, methionine (M, genetic code: AUG) Primary sequence of amino acids in polypeptide affects shape and function of proteins. Many proteins are single polypeptides. Other proteins are multiple polypeptides (form a complex), and multiple genes may be involved

4 Special Properties of Amino Acids Physical properties: a "salt-like" like behavior, a variety of structural parts which result in different polarities and solubilities Crystalline solids with relatively high melting points, and most are quite soluble in water and dinsoluble in non-polar solvents. In solution, the amino acid molecule appears to have a charge which changes with ph. Intramolecular neutralization reaction leads to a salt-like ion called a zwitterion. Amino acid has both an amine and acid group neutralized in the zwitterion i Neutral (unless there is an extra acid or base on the side chain) The amino acids in the zwitterion form: Carboxyl group can lose a hydrogen ion to become negatively charged. Amine group can accept a hydrogen ion to become positively charged.

5 Amino Acids with Hydrocarbon Chains Glycine (gly, G): simplest AA with a hydrogen atom as its side chain, fits into tight corners in the interior of a protein molecule Alanine (Ala, A): with a methyl group (CH 3 ) as its side chain 3~4 carbons long: Valine (Val, V), Leucine (Leu, L), and Isoleucine (Ile, I), hydrocarbon side chains pack AA together to form compact structures with few holes exposed to water and often interact with lipidcontaining membranes Proline (Pro, P): the bends of folded protein chains, 3-carbon-atom hydrocarbon side chain bound to both central carbon and nitrogen atom, very rigid, its presence creates a kink in a polypeptide chain

6 Aromatic Amino Acids Phenylalanine (Phe, F), Tryptophan (Trp, W) and Tyrosine (Tyr, Y): side chains of aromatic rings. Tryptophan (Trp, W) also contains a nitrogen atom in its side chain. Phenylalanine (Phe, F) and Tryptophan (Trp, W) are strongly hydrophobic. Tyrosine (Tyr, Y): less hydrophobic due to a hydroxyl group (a potential site of addition of a phosphate p group)

7 Amino Acids Containing Sulfur Cysteine (Cys, C) and Methionine i (Met, M): a sulfur atom in the side chains, hydrophobic Side chain of Cysteine is highly reactive Form a disulfide links play a special role in shaping some proteins Cysteine residues create folds and domains in the geometry of proteins. Methionine is the START codon in protein-coding genes.

8 Water-Loving (Hydrophilic) Amino Acids Serine (Ser, S) and Threonine (Thr, T): hydroxylated version of Alanine and Valine; hydroxyl groups are more reactive, hydrophilic, and potential sites of phosphate addition Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H): polar side chains containing nitrogen, highly hydrophilic Side chains of Lysine and Arginine are the longest of the 20 amino acids and normally positively charged. Histidine can be uncharged or positively charged and found in active sites of enzymes, where it can readily switch between these states to catalyze the making and breaking bonds

9 Hydrophilic Amino Acids Aspartate (Asp, D) and Glutamate (Glu, E): polar, negatively charged acidic side chains, carboxyl groups, exist at physiological ph Asparagine (Asn, N) and Glutamine (Gln, Q) are uncharged derivatives of Aspartate and Glutamate: amine group in place of carboxylate, polar molecules Amine group of Asn is a potential site of addition of sugar residues

10 20 Amino Acids 20 amino acids vary in size, charge, capacity to form hydrogen bonds with other molecules. Important determinant of the diversity of proteins Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are non- polar Hydrophobic, examples include valine, alanine, leucine, isoleucine, phenylalanine.

11 Synthesis of 20 Amino Acids Bacteria: using carbon source and ammonium ions in water to synthesize 20 amino acids Plants: using nitrogen compounds and carbohydrates to make amino acids Animals: using sugars and ammonia to make amino acids Essential amino acids: amino acids that humans cannot synthesize, e 8 amino acids, 6 of them are hdophobi hydrophobic (large hydrocarbon side chains valine, leucine, and isoleucine; aromatic side chains phenylalanine and tryptophan; sulfur- containing methionine), 2 of them are hydrophilic (threonine and lysine) Essential amino acids can be obtained from diet, such as meat, fish, milk, and eggs. (Plant sources only contain a partial set of essential amino acids, such as beans (isoleucine and lysine).)

12 The Genetic Code mrna consists of a linear sequence of such 3-letter words called codons 4 3 =64 distinct codons Protein-coding genes all begin with a START codon and terminate with a STOP codon. START codon is methionine i (M) Arginine (R), leucine (L), and serine (S) are represented by 6 codons. Synonymous y Methionine i (M) and tryptophan (W) are represented by signal codons each. First 2 letters in a codon are primary determinants of AA identity GU- (valine), GG- (glycine) UorCas2 nd nucleotide Hydrophobic GU and GC 3 rd nucleotide is U or C Same amino acid CAU and CAC (Histidine)

13 Protein-Coding Gene DNA sequence representing the beginning segment of a protein-coding gene: The complement mrna sequence: mrna codons: AUG, AAC, GUU, and UAC MNVY

14 Sickle-Cell Mutation in Hemoglobin Sequence Hemoglobin molecules exist as single, isolated units in RBC, whether oxygen bound or not, RBCs maintain basic disc shape, whether transporting oxygen or not Oxy-hemoglobin is isolated, but de-oxyhemoglobin sticks together in polymers, distorting RBC Some cells take on sickle shape

15 Protein Function Proteins are key players in our living systems. Not every protein contains all of the 20 AA types. All proteins have an AA containing sulfur Each protein folds into a unique three-dimensional structure defined by its amino acid sequence. Protein structure t has a hierarchical nature. Protein structure is closely related to its function. Protein structure prediction is a grand challenge of computational biology. Manipulation of protein sequence through changes in amino-acid sequence is a tool in modern drug design. Protein structure usually described in terms of an organizational hierarchy: Primary structure: amino-acid sequence Secondary structure: spatial arrangement of amino acids that are near one another in the linear sequence Tertiary structure: spatial arrangement of amino acids, dividing line between secondary and tertiary structure is not precise Quaternary structure: more than one polypeptide chain exhibit an additional structure

16 Protein Structure Proteins are natural polymer molecules l consisting of amino acid units Primary structure (Amino acid sequence) Secondary structure α-helix, β-sheet Tertiary structure Three-dimensional structure formed by assembly of secondary structures Quaternary structure Structure formed by more than one polypeptide chains

17 Basic Structural Units of Proteins: Secondary Structure u The chemical nature of the carboxyl and amino groups of all amino acids permit hydrogen bond formation (stability) and hence defines secondary structures within the protein. The Rgrouphas an impact on the likelihood of secondary structure formation (Proline is an extreme case) Helices and sheets: regular secondary structures, but irregular secondary structures exist and can be critical for biological function α-helix turn right or left from N to C terminal: only right-handed are observed in nature, can be stretched for breaking and rearranging H- bond Elastic β-plated sheet: hydrogen bonding between elements and peptide linkages when the protein chains extend and lie next to another, forming flat sheets Secondary structures, α-helix and β-sheet, have regular hydrogen-bonding patterns. α-helix β-sheet

18 Three-Dimensional Structure of Proteins Tertiary structure: While backbone interactions define most of the secondary structure interactions, it is the side chains that define the tertiary interactions Disulphide p linkages between cysteines form the strongest covalent bond in tertiary linkages Quaternary structure: More than one polypeptide chain Noncovalent forces hold multiple polypeptide chains together to form protein complex Ionic bonds (i.e. Van der Waals forces: transient, weak electrical attraction of one atom for another), hydrophobic interactions (clustering of nonpolar groups), hydrogen bonds Quaternary structure Tertiary structure

19 3D Molecular Graphics of Scallop Myosin I α-helix: corkscrew-like righthanded, side chains (circular cylinder) extending outward from the peptide backbone of the helix β-plated sheet: aflat arrow pointing toward the carboxyl end of the peptide p C N

20 Gene A human cell contains about 100 million proteins of about 10,000 types These cells all possess the same protein-coding genes (~30,000), 000) but different cell types express different proteins of these genes Complexity of the organism Gene in vertebrate: Short sequences (exons) + long noncoding sequences (introns) Various spatial combinations of these exons correspond to different proteins. A gene can code for multiple proteins in higher forms of life. Complicating proteins: proteins with carbohydrate, lipid, phosphate, p and other types of attachments

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