Download Amino Acids and Peptides-chap 3

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; Damino 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?
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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 acids
Why some amino acids are found less
commonly in proteins?
 Produced by
modification of
parent amino acid
in posttranslation
Uncommon amino acids
Why 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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