Proteins

Proteins (Greek = “of first importance”) Functions: – Structure - skin, bones, hair, fingernails – Catalysis - biological catalysts are enzymes – Movement - muscle: actin and myosin – Transport - hemoglobin, transport thru membranes

Proteins Functions: – Hormones - insulin, oxytocin, HGH, etc. – Protection - antigen-antibody reactions, fibrinogen in clotting – Storage - casein in milk, ferritin in liver-stores iron – Regulation - control in expression of genes

Proteins Protein types: – 9000 different proteins in a cell – Fibrous Protein Insoluble in H 2 O Used mainly for structural purposes – Globular Protein Partly soluble in H 2 O Usually not used for structural purposes

Proteins are Natural Polymers Proteins are constructed in the body from many repeating units call amino acids Just like other polymers the amino acids (monomers) are joined together to make long chains (polymers) – but we call them proteins instead All of the polymer information applies to proteins – cross linking, rings, polarity etc.

Amino Acids The Building Blocks of proteins – Contains an amino group and an acid group – Nature synthesizes about 20 common AA – All but one (proline) fit this formula: – AA Proline:

Amino Acids Amino Acids (AA) – The twenty common are Called alpha amino acids – One and three letter codes given to 20 common AA – All but glycine (where R=H) exist as a pair of enantiomers nature usually produces the L amino acid

Amino Acids Amino Acids (AA) – Sometimes classified as AA with: nonpolar R groups polar but neutral R groups acidic R groups basic R groups

Zwitterions An acid -COOH and an amine -NH 2 group cannot coexist The H + migrates to the -NH 2 group COO - and NH 3 + are actually present, called a “Zwitterion”

Zwitterions Zwitterion = compound where both a positive charge and a negative charge exist on the same molecule AA are ionic compounds They are internal salts In solution their form changes depending on the pH AA’s

Zwitterions pH = 1-5 excess H + excess OH - pH = more basic more acidic AA’s

Zwitterions pH = 1-5 excess H + excess OH - pH = more basic more acidic at pI (isoelectric point) charge = 0 AA’s

pI The pI is the “isoelectric point” The pI is the pH where NO charge is on the AA: at pI charge = 0 (Not necessarily at a neutral pH)

Amino Acids The amino acids obtained by hydrolysis of proteins differ in respect to R (the side chain). The properties of the amino acid vary as the structure of R varies. CCOO – RR H H3NH3NH3NH3N +

Amino Acids Glycine is the simplest amino acid. It is the only one in the table that is achiral. In all of the other amino acids in the table the  carbon is a stereogenic center. CCOO – H H H3NH3NH3NH3N + Glycine (Gly or G)

Glycine (Gly or G)

Amino Acids CC O O – CH 3 H H3NH3NH3NH3N + Alanine (Ala or A)

Alanine (Ala or A)

Amino Acids CC O O – CH(CH 3 ) 2 H H3NH3NH3NH3N + Valine (Val or V)

Valine (Val or V)

Amino Acids CC O O – CH 2 CH(CH 3 ) 2 H H3NH3NH3NH3N + Leucine (Leu or L)

Leucine (Leu or L)

Amino Acids CC O O – CH 3 CHCH 2 CH 3 H H3NH3NH3NH3N + Isoleucine (Ile or I)

Isoleucine (Ile or I)

Amino Acids CC O O – CH 2 OH H H3NH3NH3NH3N + Serine (Ser or S)

Serine (Ser or S)

Amino Acids CC O O – CH 3 CHOH H H3NH3NH3NH3N + Threonine (Thr or T)

Threonine (Thr or T)

Amino Acids CC O O – CH 3 SCH 2 CH 2 H H3NH3NH3NH3N + Methionine (Met or M)

Methionine (Met or M)

Amino Acids CC O O – CH 2 SH H H3NH3NH3NH3N + Cysteine (Cys or C)

Cysteine (Cys or C)

Amino Acids Aspartic Acid CCOO – H H3NH3NH3NH3N + OCCH 2 O – (Asp or D)

Aspartic Acid (Asp or D)

Amino Acids Glutamic Acid CCOO – H H3NH3NH3NH3N + OCCH 2 CH 2 O – (Glu or E)

Glutamic Acid (Glu or E)

Amino Acids Proline CCOO – CH 2 H H2NH2NH2NH2N + H2CH2CH2CH2C CH2CH2CH2CH2 (Pro or P)

Proline (Pro or P)

Amino Acids Phenylalanine (Phe or F)

Phenylalanine (Phe or F)

Amino Acids Tyrosine (Tyr or Y)

Tyrosine (Tyr or Y)

Amino Acids Histidine (His or H)

Histidine (His or H)

Cysteine The AA Cysteine exists as a dimer: a disulfide linkage AA’s

Peptides AA are also called peptides They can be combined to form... AA’s

Peptides AA are also called peptides They can be combined to form a dipeptide. a peptide bond

Peptides Known as a “dipeptide” a peptide bond amine end acid end glycylalanine (Gly-Ala), a dipeptide

Peptides Glycylalanine is not the same as Alanylglycine glycylalanine alanylglycine

Peptides Synthesis of Alanylglycine alanylglycine

Polar (Hydrophilic) R Groups Serine (Ser) Cysteine (cys) Glutamine (Gln) Asparagine (Asn) Tyrosine (Tyr) Threonine (Thr)

Peptides Addition of peptides (head to tail) – Formation of: dipeptides tripeptides tetrapeptides pentapeptides polypeptides PROTEINS AA’s

Student Practice Show the product for the following combination of amino acids Glu – Pro – His Pro – Asn – Leu Val – Ala – Trp

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Proteins Proteins usually contain about 30+ AA AA known as residues – One letter abbreviations G, A, V, L – Three letter abbreviations Gly, Ala, Val, Leu N terminal AA (amine end) on LEFT C terminal AA (carboxyl end) on RIGHT glycylalanineGly-AlaG-A AA’s

Polypeptides peptide bonds side chains amino acid residues AA’s

Solubility Polypeptides or Proteins – If there is a charge on a polypeptide, it is more soluble in aqueous solution – If there is NO CHARGE (neutral at pI), it is LEAST SOLUBLE in solution charged

Protein Structure Primary Structure 1 o – Linear sequence of AA Secondary Structure 2 o – Repeating patterns (  helix,  pleated sheet) Tertiary Structure 3 o – Overall conformation of protein Quaternary Structure4 o – Multichained protein structure

Protein Structure Primary Structure 1 o – Linear sequence of AA AA 1AA 2AA 3AA 4AA 5AA 6 With any 6 AA residues, the number of possible combinations is 6 x 6 x 6 x 6 x 6 x 6 = AA’s

Protein Structure Primary Structure AA 1AA 2AA 3AA 4AA 5AA 6 With any 6 of the 20 common AA residues, the number of possible combinations is 20 x 20 x 20 x 20 x 20 x 20 = 64,000,000 (and this is not nearly large enough to be a protein!) AA’s

Protein Structure Primary Structure – A typical protein could have 60 AA residues. This would have possible primary sequences = This results in more possibilities for this small protein than there are atoms in the universe!

Protein Structure Primary Structure – Sometimes small changes in the 1 o structure do not alter the biological function, sometimes they do. AA’s

Changes and Effect of AA change Cattle and hog insulin is used for humans but is different Sickle cell anemia – only one change in an amino acid – changes the hemoglobin From yahoo images

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Protein Structure Secondary Structure – Repeating patterns within a region – Common patterns  helix  pleated sheet – Originally proposed by Linus Pauling Robert Corey AA’s

Protein Structure Secondary Structure  helix – Single protein chain – Shape maintained by intramolecular H bonding between -C=O and H-N- – Helical shape  helix is clockwise AA’s

Protein Structure Secondary Structure  pleated sheet – Several protein chains – Shape maintained by intramolecular H bonding and other attractive forces between chains – Chains run anti-parallel and make U turns at ends AA’s

Protein Structure Secondary Structure Random Coils – Few proteins have exclusively  helix or  pleated sheet – Many have non-repeating sections called: Random Coils AA’s

Collagen Protein Structure Secondary Structure Triple Helix of Collagen – Structural protein of connective tissues bone, cartilage, tendon aorta, skin – About 30% of human body’s protein – Triple helix units = tropocollagen AA’s

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Tertiary Structure – The Three dimensional arrangement of every atom in the molecule – Includes not just the peptide backbone but the side chains as well – These interactions are responsible for the overall folding of the protein – This folding defies its function and it’s reactivity AA’s

Tertiary Structure The Tertiary structure is formed by the following interactions: Covalent Bonds Hydrogen Bonding Salt Bridges Hydrophobic Interactions Metal Ion Coordination AA’s

Tertiary Structure –Covalent Bonding The most common covalent bond in forming the tertiary structure is the disufide bond It is formed from the disulfide Interaction of cysteine

Tertiary Structure –Hydrogen Bonding Anytime you have a hydrogen connected to a F O of N – you can get hydrogen bonding These interactions can occure on the side chain, backbone or both

Tertiary Structure –Salt Bridge Salt bridges are due to charged portions of the protein. Opposite charges will attract and Form ionic bonds Some examples are the NH 3 + and COO - areas of the protein

Tertiary Structure –hydrophobic interactions Because the nonopolar groups will turn away from the water and the polar groups toward it, hydrophobic interactions take place. These interactions are strong enough to help define the overall structure of a protein

Tertiary Structure –Metal Ion Coordination Two side chains with the same charge would normally repel each other However, if a metal is placed between them, they will coordinate to the meal and be connected together. These metal coordinations are Important in tertiary structure formation

Tertiary Structure

Quaternary Structure – Highest level of organization – Determines how subunit fit together – Example Hemoglobin (4 sub chains) 2 chains 141 AA 2 chains 146 AA - Example - Collagen

Denaturation – Any physical or chemical agent that destroys the conformation of a protein is said to “denature” it – Examples: Heat (boil an egg) to gelatin Addition of 6M Urea (breaks H bonds) Detergents (surface-active agents) Reducing agents (break -S-S- bonds)

Denaturation – Examples: Acids/Bases/Salts (affect salt bridges) Heavy metal ions (Hg 2+, Pb 2+ ) – Some denaturation is reversible Urea (6M) then add to H 2 O – Some is irreversible Hard boiling an egg

Denaturation