Amino Acids & ProteinsAmino Acids & Proteins

Shu-Ping Lin, Ph.D.Instit te of Biomedical Enginee ingInstitute of Biomedical Engineering

E-mail: splin@dragon.nchu.edu.twWebsite: http://web nchu edu tw/pweb/users/splin/Website: http://web.nchu.edu.tw/pweb/users/splin/

Date: 10.13.2010Date: 10.13.2010

Amino AcidsProteins are the basis for the major structural components of animaland human tissue Linear chains of amino acids residuesAmino Acids (AA): 1 central carbon atom + 4 subgroups {aminoAmino Acids (AA): 1 central carbon atom + 4 subgroups {aminogroup (NH2), carboxyl group (COOH), hydrogen atom, anda 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 AADifferent R groups Different properties and AAMirror-image forms (stereoisomers) L and D-isomersOnly 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 proteins300 AA in nature, but only 20 of these in proteinsNot every protein contains all of the 20 AA types.All proteins have an AA containing sulfur

Make peptides and Proteins

Synthesis of Polypeptides & ProteinsAmino group join to carboxyl group and lose one water moleculeAmino 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 ResultForm backbone of the polypeptides and expose side chains R Result in proteins with intricate 3D structures and a remarkable range of functionsPolypeptides: 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 aminoFirst/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 f t i M t i i l l tid Oth t iof proteins. Many proteins are single polypeptides. Other proteins are

multiple polypeptides (form a complex), and multiple genes may be involved

Special Properties of Amino AcidsPhysical properties: a "salt-like" behavior a variety of structural parts whichPhysical 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

l bl i d i l bl i l lsoluble in water and insoluble in non-polar solvents.In solution, the amino acid molecule appears to have a charge which changes with pH.g pIntramolecular neutralization reaction leads to a salt-like ion called a zwitterion.A i id h b th i d id t li d i th itt iAmino 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 ChainsGlycine (gly, G): simplest AA with a hydrogen atom as its side chain, fits y (g y, ) p y g ,into tight corners in the interior of a protein moleculeAlanine (Ala, A): with a methyl group (CH3) as its side chain3 4 b l V li (V l V) L i (L L) d I l i3~4 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 membranesProline (Pro, P): the bends of folded protein chains, 3-carbon-atom hydrocarbon side chain bound to both central carbon and nitrogen atomhydrocarbon side chain bound to both central carbon and nitrogen atom, very rigid, its presence creates a kink in a polypeptide chain

Aromatic Amino AcidsPhenylalanine (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)g p ( p p p g p)

Amino Acids Containing SulfurC t i (C C) d M thi i (M t M) lf tCysteine (Cys, C) and Methionine (Met, M): a sulfur atom in the side chains, hydrophobicSide chain of Cysteine is highly reactive Form a disulfideSide chain of Cysteine is highly reactive Form a disulfide links play a special role in shaping some proteinsCysteine residues create folds and domains in the geometryCysteine residues create folds and domains in the geometry of proteins.Methionine is the START codon in protein-coding genes.Methionine is the START codon in protein coding genes.

Water-Loving (Hydrophilic) Amino AcidsSerine (Ser S) and Threonine (Thr T): hydroxylated version ofSerine (Ser, S) and Threonine (Thr, T): hydroxylated version of Alanine and Valine; hydroxyl groups are more reactive, hydrophilic, and potential sites of phosphate additionLysine (Lys, K), Arginine (Arg, R), and Histidine (His, H): polar side chains containing nitrogen, highly hydrophilicSide chains of Lysine and Arginine are the longest of the 20 amino acidsSide 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 AcidsAspartate (Asp, D) and Glutamate (Glu, E): polar, negatively charged acidic side chains, carboxyl groups, exist at physiological pHphysiological pHAsparagine (Asn, N) and Glutamine (Gln, Q) are uncharged derivatives of Aspartate and Glutamate: amineuncharged derivatives of Aspartate and Glutamate: aminegroup in place of carboxylate, polar moleculesAmine group of Asn is a potential site of addition of sugarAmine group of Asn is a potential site of addition of sugar residues

20 Amino Acids 20 amino acids vary in size, charge, capacity to formcapacity to formhydrogen bonds with other molecules. ImportantImportant determinant of the diversity of proteinsSide chains whichSide chains which have pure hydrocarbon alkyl groups (alkanegroups (alkane branches) or aromatic (benzene rings) are non-gs) a e opolarHydrophobic, examples include pvaline, alanine, leucine, isoleucine, phenylalanine.

Synthesis of 20 Amino AcidsBacteria: using carbon source and ammonium ions in water to synthesize 20 amino acidsPlants: using nitrogen compounds and carbohydrates to make amino acids

l d k dAnimals: using sugars and ammonia to make amino acidsEssential amino acids: amino acids that humans cannot

nthe i e 8 mino id 6 of them e h d ophobi (l gesynthesize, 8 amino acids, 6 of them are hydrophobic (large hydrocarbon side chains valine, leucine, and isoleucine; aromatic side chains phenylalanine and tryptophan; sulfur-aromatic side chains phenylalanine and tryptophan; sulfurcontaining 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 CodemRNA consists of a linear sequence of such 3-letter words called codonsmRNA consists of a linear sequence of such 3 letter words called codons43=64 distinct codonsProtein-coding genes all begin with a START codon and terminate with a STOP d START d i thi i (M)STOP codon. START codon is methionine (M)Arginine (R), leucine (L), and serine (S) are represented by 6 codons. Synonymous M thi i (M) dy y Methionine (M) and

tryptophan (W) are represented by signal codons each.First 2 letters in a codon are primary determinants of AAprimary determinants of AA identity GU- (valine), GG-(glycine)U or C as 2nd nucleotideU or C as 2nd nucleotide Hydrophobic GU and GC3rd nucleotide is U or C Same amino acid CAU and CAC (Histidine)

Protein-Coding GeneDNA sequence representing the beginning segment of a

t i diprotein-coding gene:

Th l t RNAThe complement mRNA sequence:

mRNA codons: AUG, AAC, GUU, and UAC MNVY

Sickle-Cell Mutation in Hemoglobin SequenceHemoglobin Sequence

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

Protein FunctionProteins are key players in our living systemsProteins are key players in our living systems.Not every protein contains all of the 20 AA types.All proteins have an AA containing sulfurp gEach protein folds into a unique three-dimensional structure defined by its amino acid sequence.P t i t t h hi hi l tProtein structure has a hierarchical nature.Protein structure is closely related to its function.Protein structure prediction is a grand challenge of computational biology.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 oneSecondary structure: spatial arrangement of amino acids that are near one another in the linear sequenceTertiary structure: spatial arrangement of amino acids, dividing line between secondary and tertiary structure is not precisesecondary and tertiary structure is not preciseQuaternary structure: more than one polypeptide chain exhibit an additional structure

Protein StructureProteins are natural

l l lpolymer molecules consisting of amino acid unitsacid units

Primary structure (Amino acid sequence)

Secondary structure -helix, -sheet

Tertiary structure Three-dimensional f d b bl fstructure formed by assembly of

secondary structures

Quaternary structureStructure formedQuaternary structure Structure formed by more than one polypeptide chains

Basic Structural Units of Proteins: Secondary StructureSeco da y S uc u e

Secondary structures, -helix and -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 hydrogen-bonding patterns.hydrogen bond formation (stability) and hence defines secondary structures within the protein. The R group has an impact on the likelihoodThe R group has an impact on the likelihood of secondary structure formation (Proline is an extreme case)Helices and sheets: regular secondary

-helixHelices and sheets: regular secondary structures, but irregular secondary structures exist and can be critical for biological function-helix turn right or left from N to C terminal:

-sheet

-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 Elasticbond Elastic-plated sheet: hydrogen bonding betweenelements and peptide linkages when the protein chains extend and lie next to anotherprotein chains extend and lie next to another, forming flat sheets

Three-Dimensional Structure of ProteinsTertiary structure:

While backbone interactions define most of the secondary structure interactions, it is the side chains that define the tertiary interactionsDisulphide linkages between cysteines form the strongest covalent bond in p g y g

tertiary linkagesQuaternary structure:

More than one polypeptide chainMore 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 interactionselectrical attraction of one atom for another), hydrophobic interactions (clustering of nonpolar groups), hydrogen bonds

Quaternary structure

Tertiary structure

3D Molecular Graphics of Scallop Myosin IScallop Myosin I

helix: corkscrew like right-helix: corkscrew-like right-handed, side chains (circular cylinder) extending outward y ) gfrom the peptide backbone of the helix plated sheet: a flat arrow-plated sheet: a flat arrow pointing toward the carboxyl end of the peptidep p

C

N

GeneA human cell contains about 100 million proteins of about 10,000 types These cells all possess the same protein-coding

( 30 000) b t diff t ll t diff tgenes (~30,000), but different cell types express different proteins of these genes Complexity of the organismGene in vertebrate: Short sequences (exons) + long noncodingGene in vertebrate: Short sequences (exons) + long noncoding sequences (introns)Various spatial combinations of these exons correspond toVarious spatial combinations of these exons correspond to different proteins.A gene can code for multiple proteins in higher forms of lifeA gene can code for multiple proteins in higher forms of life.Complicating proteins: proteins with carbohydrate, lipid, phosphate, and other types of attachmentsp p , yp