Shu-Ping Lin, Ph.D.

Institute of Biomedical Engineering E-mail: splin@dragon.nchu.edu.tw

Website: http://web.nchu.edu.tw/pweb/users/splin/

Macromolecules of Life -3

Amino Acids & Proteins

mailto:splin@dragon.nchu.edu.twhttp://web.nchu.edu.tw/pweb/users/splin/

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 (—NH2), 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

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

Special Properties of Amino Acids Physical properties: a "salt-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 insoluble 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 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.

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 (CH3) 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 lipid-containing 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

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 group)

Amino Acids Containing Sulfur Cysteine (Cys, C) and Methionine (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.

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

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

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.

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, 8 amino acids, 6 of them are 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).)

The Genetic Code mRNA consists of a linear sequence of such 3-letter words called codons

43=64 distinct codons

Protein-coding genes all begin with a START codon and terminate with a STOP codon. START codon is methionine (M)

Arginine (R), leucine (L), and serine (S) are represented by 6 codons.

Synonymous Methionine (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)

U or C as 2nd nucleotide Hydrophobic GU and GC

3rd nucleotide is U or C Same amino acid CAU

and CAC (Histidine)

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

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

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 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

Protein Structure

Proteins are natural polymer molecules 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）

Basic Structural Units of Proteins: Secondary Structure

α-helix

β-sheet

Secondary structures, α-helix and β-sheet, have regular hydrogen-bonding patterns.

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 R group has 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

Three-Dimensional Structure of Proteins

Tertiary structure

Quaternary structure

Tertiary structure: While backbone interactions define most of the secondary structure interactions, it is the side chains that define the tertiary interactions Disulphide 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

3D Molecular Graphics of Scallop Myosin I

α-helix: corkscrew-like right-handed, side chains (circular cylinder) extending outward from the peptide backbone of the helix

β-plated sheet: a flat arrow pointing toward the carboxyl end of the peptide

N

C

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), 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, and other types of attachments