Amino Acids and Peptides

Chapter 3

Why is it important to specify the three dimensional structure of amino acids?

Three dimensional structure of amino acids

α-carbon has amino group and carboxyl group

R-group – identity to amino acid

Also bond to hydrogen

What is Stereochemistry?

Nonsuperimposable mirror images – Chiral All protein-derived amino acids have at least one

stereocenter (the α-carbon) and are chiral (stereoisomers) – except glycine

Two stereoisomers of amino acids are designated L- or D-

Amino acid structures (figure 3.3)

The position of amino group on left or right side of alpha carbon determines the L or D designation

L-amino acids are found in all proteins; D-amino acid image found in proline

D-amino acids are found in nature Three letter or one-letter codes – refer to

amino acids Memorize table 3.1

Why are amino acid side chains so important?

Side chains – classification of amino acids Polar and nonpolar nature of side chain Acidic or basic group in side chain Nature of functional groups in side chains Side chain – simplest in glycine Can be larger and complex Carbon atoms – β-, γ-, ε-, δ- and ω- carbons

(refer to lysine in figure 3.3)

Which amino acids have nonpolar side chains? (Group 1)

Nonpolar side chains – Ala, Val, Leu, Ile, Pro, Phe, Trp and Met

Ala, Val, Leu, Ile. Pro – aliphatic hydrocarbon group- (absence of a benzene ring)

- Proline has cyclic aliphatic structure

Which amino acids have nonpolar side chains? (Group 1)

Phenylalanine – hydrocarbon is aromatic (contains cyclic group similar to benzene ring)

Trp – aromatic indole ring side chain

Met – Sulfur + aliphatic hydrocarbon groupings in side chain

Which amino acids have electrically neutral polar side chains? (group 2)

Neutral polar side chains – electrically neutral (uncharged) at neutral pH

Ser, Thr, Tyr, Cyc, Glu, Asn

Which amino acids have electrically neutral polar side chains? (group 2)

Ser, Thr – polar hydroxyl (-OH) group

Tyr – hydroxyl group bonded to aromatic hydrocarbon group

Cys – thiol group (-SH)

Gln, Asn – amide bonds

Which amino groups have carboxyl groups in their side chains? (Group 3)

Acidic side chains – Glutamic acid (Glu) and Aspartic acid (Asp)

Carboxyl group (in addition to one already present)

Lose a proton to form – carboxylate anion Negatively charged at neutral pH

Which amino acids have basic side chains?

Basic side chains – His, Lys, Arg Positively charged at or near neutral pH Lys – NH3 group is attached to an aliphatic

hydrocarbon chain Arg – Guanidino group His – Imidazole group

Amino acid summary

α carbon present in 20 amino acids α amino group is primary (19 aa) and secondary

in proline α carbon is stereo centre in all except glycine Isoleucine and threonine – second stereo center Letter codes in table 3.1

Uncommon amino acidsWhy some amino acids are found less commonly in proteins?

Produced by modification of parent amino acid in posttranslation

Uncommon amino acidsWhy amino acids are found less commonly in proteins?

Hydroxylysine and Hydroxyproline differ from parent by having hydroxyl groups on their side chains- found in connective-tissue proteins-collagen

Thyroxine has extra iodine-containing aromatic group- found in thyroid glands

What are zwitterions? Amino acids without charged groups on their side

chains – exist in neutral solution – zwitterions - with no net charge

Zwitterions have equal positive and negative charges at neutral pH – electrically neutral

Why aminoacids can act as both acids and bases?

The pKa values of α carboxyl groups are 2

The pKa values of amino group are 9 to 10.5

The classification of aa as acidic or basic depends on pKa of side chain as well as chemical nature of group

Why aminoacids can act as both acids and bases?

Histidine, Lysine and arginine – basic aa – amino group - high pKa

Aspartic acid and glutamic acid – acidic aa – carboxylic side chains – low pKa

Have titratable protons. Some side chains do as well

What happens when we titrate an amino acid?

Titration curve indicates reaction of each functional group with hydrogen ion

Titration of alanine with NaOH

At low pH – uncharged carboxyl group and positively charged amino group

Alanine has a positive charge of 1

As base is added, carboxyl group loses proton – negatively charged carboxylate group and pH increases

Titration of alanine with NaOH

Alanine has no net charge

pH increases with addition of base – aminogroup loses it proton

Alanine has negative charge of 1

Diprotic acid

What is Isoelectric point?

Positive and negative charges are equal – no net charge – Isoelectric point or pH

pI = pKa1 + pKa2

2 Determines properties of amino acids and proteins

Which groups on amino acids react to form a peptide bond?

Individual amino acids can be linked by forming covalent bonds

PEPTIDE (amide) bond is formed between α carboxyl group of one amino acid and α amino group of another amino acid

Dipeptide, tripeptide, polypeptide (> 100 amino acids)

Geometry of peptide bond The four atoms of a peptide bond joined by two alpha

carbon atoms – lie in planar plane with bond angles of 120 about C and N

Represented as a hybrid of two contributing structures – resonance structures

What are some biological functions of small peptides?

Marked physiological effects in organisms Naturally occurring dipeptide – carnosine is found in

muscle tissue

Glutathione – scavanger of oxidizing agents

Oxytocin and vasopressin – hormones

Enkephalins – naturally occurring painkillers

Carnosine

Carnosine has alternative name – beta alanyl-L-histidine

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