Amino acids are the building blocks of proteins and peptides. They contain non-polar, polar, and charged R groups. Peptides are formed through condensation reactions between amino acids, linking them through peptide bonds. There are four levels of protein structure - primary, secondary, tertiary, and quaternary. The secondary structure involves folding into alpha helices or beta sheets. The alpha helix is stabilized by hydrogen bonds between residues four places apart in the sequence. Tertiary structure describes the three-dimensional folding of the polypeptide chain. Quaternary structure involves the interaction of multiple polypeptide chains in a protein.

1. Amino Acid, Peptides
(biomedical importance)
BIOCHEMISTRY
JSMU
16-11-2013

2. ANATOMY OF AN AMINO
ACID

3. Non-polar amino acids (Revisit)

4. Polar, non-charged amino acids

5. Negatively-charged amino acids

6. Positively-charged amino acids

7. Nomenclature
C
R
H
COOHH2N
α

8. 1. FUNCTIONS OF AMINO ACIDS
Amino Acid (AA) - Protein
Peptides (from the Greek, "digestible"), are formed through
condensation of amino acids through peptide bonds.
: basic unit
: amino acid chain, containing 2 or more AA.
: containing < 100 AA.
: > 100 AA.

9. Peptide bond: a chemical bond formed between two AA
- the of one amino acid reacts with
- the of the other amino acid,
- releasing a molecule of .
This is a condensation (dehydration) reaction.

10. A peptide bond
(amide bond)
Covalent chemical bond formed between two
molecules when the carboxyl group of one
molecule reacts with the amino group of the other
molecule, causing the release of a molecule of
water (H2O), hence the process is a dehydration
synthesis reaction (also known as a condensation
reaction), and usually occurs between amino acids.
The resulting C(O)NH bond is called a peptide
bond, and the resulting molecule is an amide.

12. It is the partial double-bond character of the
peptide bond that defines the conformations a
polypeptide chain may assume.
It is shorter then a single bond
Rigid & planar
The group can take one of two major
configurations:
Cis or Trans

13. CIS CONFIG

14. TRANS CONFIG

16. Peptide
Nomenclature:
Direction of codons and amino acids
Language: meaning
Two ends (Amino and Carboxylic)
How to name
ANGIOTENSIN-II Asp-Arg-Val-Tyr-Ile-His-Pro-Phe

17. FUNCTIONS OF AMINO ACIDS
Glycine
(sweet)
Heme synthesis
Purine synthesis
Glutathione synthesis
Conjugation with bile acids
Detoxification: e.g., benzoic acid
Inhibitory neurotransmitter

18. Methionine
S~adenosyl methionine Contributes for spermine &
spermidine
synthesis(polyamines)
Cell proliferation & growth
Methyl group donor
Remaining carbon
converts to succinyl CoA

19. Cysteine:
Component of Coenzyme A
Precursor of Taurine
Histidine: Decarboxylation gives HISTIMINE
Arginine:
Nitric oxide ( NO )
Arginine phosphate
Creatine phosphate
Creatinine

20. Tryptophan Serotonin
A potent vasoconstrictor
Stimulator of smooth muscle contraction
Anti depressant
Tyrosine: Thyroid hormone
Noradrenaline
Adrenaline
Melatonin

21. Non-Standard amino
acids
• 4-Hydroxyproline, a derivative of proline,
• 5- Hydroxylysine, derived from lysine. Collegen
• Methyl-lysine Myosin
• Carboxyglutamate- Prothrombin
• Desmosine- Elastin
• Selenocysteine- active site for enzymes
• Ornithine & Citrulline – urea & arginine
synthesis

22. • Homocysteine
• GABA-(γ-amino-butyric acid)
• DOPA
• Iodinated amino acids
• Pantothenic acid
• Argininosuccinic acid
• β-alanine

23. Use of Amino Acids
Aspartame: Artificial sweetener
(aspartyl-phenylalanine-1-methyl ester).
5-HTP: has been used to treat neurological
problems with PKU (Phenylketonuria) &
Depression. (5-hydroxytryptophan)
L-DOPA: is a drug used to treat Parkinsonism.
(L-dihydroxyphenylalanine)
Monosodium glutamate: is a food additive to
enhance flavor.

24. Peptides
• Cytochrome-C
• Hemoglobin
• Myoglobin
• Ribonucleases A
• Apolipoprotein B
• RNA Polymerases

25. Non- standard amino acids:
These are either synthesized in the cells or the derivatives
of standard AA.
Hydroxy Lysine
Hydroxy Proline
Present in collagen, a fibrous protein of
connective tissues.
Methyl lysine: Present in myosine
Gamma carboxyglutamate: Present in Ca++
binding proteins
Ornithine
Citrulline Precursor of arginine, urea, spermine & spermidine

26. Desmosine: Formed by the condensation of FOUR Lysine
residues.
Present in Elastin, a fibrous protein.
Nor epinephrine,
Epinephrine,
Thyroxin (T4)
Triiodothyronine (T3)

27. Small Peptides:
Aspartam: Artificial sweetner.
A dipeptide: Aspartyl-phenylalanyl methyl ester.
Oxytocin: Contains 9 AA.
A posterior pituitary hormone
causing uterine contraction.
Bradykinin Contains 9 AA.
Inhibitor of inflammation
Glutathione
Detoxification of xenobiotics, H2O2.
Intracellular reductant
Transport of AA across the cell membrane.
A tripeptide

28. Thyrotropin Releasing Factor ( TRF ):
Contains 3 AA.
Synthesized in hypothalamus
Stimulates anterior pituitary
For Thyrotropin secretion.
Glucagon:
Contains 29 AA
Hyperglycemic factor
ACTH: 29 AA, acts on adrenal cortex for cortisol secretion
Neuropeptides:

29. 3. FUNCTIONS OF AMINO ACIDS
zwitterion & buffering
Zwitter Ion:
At physiological PH (7.4)
• COOH group (weak acid/proton donor) is dissociated forming
a negatively charged carboxylate ion (COO-)
• amino group (weak base/proton acceptor) is protonated
forming positively charged ion (NH3+) forming.
The molecule attains both +ve and –ve charges with NO NET
charge
A zwitterion can act as either an acid (proton donor) or a
base (proton acceptor)

30. zwitterion & buffering

33. Partial double bond character of peptide bond:
C
N
O
H
N
O
H
This character of peptide bond restrict its free rotation

34. C
N
C
C
N
C
C
N
Polypeptide backbone
C
N
C
C
N
C
C
N
α α
α α
O
O
O
RH
H
R
H
H
H

35. C
N
C
C
N
C
C
N
α α
O
O
O
RH
H
R
H
H
H
It has three covalent bonds:
Co → N
Peptide bond
(No free rotation)
Cα→ N Cα→ Co
Free rotation
phi angle
─ 57
psi angle
─ 47

36. PROTEIN STRUCTURE
There are FOUR levels of protein structure:
PRIMARY STRUCTURE
SECONDARY STRUCTURE
TERTIARY STRUCTURE
QUATERNAEY STRUCTURE

38. PRIMARY STRUCTURE
It is the sequence of the amino acid in a protein molecule
It is according to the genetic codes, present in gene
for a particular protein.

39. SECONDARY STRUCTURE
The folding of short contiguous segments
( 3 – 30 residues ) of a polypeptide into a
geometrically ordered units.
Two types:
1. α- Helix
2. β- Pleated sheet

40. The polypeptide back bone is twisted by an equal
amount about each α- carbon
1. α- Helix
In one complete turn there are 3.6 amino acids
with a pitch of 0.54 nm
The R-groups face outward

41. 0.54 nm
3.6 AA

42. The α- helix is stabilized by :
1. Hydrogen bonds formed between C=O and NH
of each fourth residue.
1 – 2 – 3 – 4 – 5 – 6 – 7 – 8 – 9 – 10 – 11 -----
=O
=O
=O
=O
=O
=O
=O
=O
=O
=O
N
H
N
H
N
H
N
H
N
H
N
H
N
H
N
H
N
H
N
H

45. α- helix is also stabilized by the van-der Waal
interactions among the different groups.
The proline and glycine interfere the α- helix
either by giving a turn or bend.
In α- helix, the hydrophobic R-groups acquire the
interior while the hydrophilic R-groups acquire the
exterior.

46. 2. β- Pleated Sheet:
Occurs in proteins contain several segments or chains
The amino acids form a zigzag pattern.
The polypeptide backbone is highly extended.
The structure is stabilized by H-bonds formed between
the C=O and NH groups of adjacent segments and
chains.

47. Two Types:
a) Parallel:
b) Antiparallel:

48. Tertiary structure:
Entire three dimensional conformation of a polypeptide
chain indicating how helices, sheets, bends turns and
loops assemble to form DOMAIN and how different
domains interact with each other in space.
The tertiary structure protein is also called
NATIVE protein.
Structure is stabilized by:
H- bonds and salt bridges between COOH of Asp and Glu
and NH2 group of Arg, Lys and His.
Hydrophobic interaction among the hydrophobic
R- groups which acquire the interior.

49. Quaternary structure:
Proteins having more than one polypeptide chains
acquire quaternary structure.
H- bonds, salt bridges and hydrophobic interaction
Stabilize the structure.