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(BCHM) D S01 T02 Amino Acids Peptides Proteins
(BCHM) D S01 T02 Amino Acids Peptides Proteins
Trans #2
Dr. Phyllis Rio
[SUBJECT]
[Name of Lecturer]
OUTLINE
ACID-BASE PROPERTY
• AA have both the acidic, carboxyl group (α -COOH) and basic,
amino group (α-NH2) components
• These groups are capable of ionizing
• As R-groups of acidic and basic AA as well as Cysteine and
Tyrosine
• Carboxylic group is more acidic than amino group; it gives off
H+ first Figure 7. Ionization state at different pH
2. OXIDATIVE DEAMINATION
• α-amino group is removed from an amino acid to
form a ketoacid and ammonia
• Glutamic acid is the most common amino acid
that undergoes this reaction
C. CHEMICAL REACTIONS
II. PROTEINS
• Macromolecules with nitrogenous compounds
• Peptide – short chain of amino acid
• Peptides are used as:
1. Hormones (e.g. insulin)
2. Neurotransmitters (e.g. GABA)
3. Antibiotics (e.g. Gramicidin A)
4. Regulators (e.g. Glutathione)
5. Anti-tumor agent (e.g. Belomycin)
Figure 18. Formation of N-glycosidic bond between Asparagine and N-
acetylglucosamine forming a glycoprotein • By convention, N-terminal end is written at the left while
the C-terminal end is written at the right.
4. REACTION OF SULFHYDRYL GROUP • Polymerization of amino acids through peptide bonds to
• Sulfhydryl group of cysteine forms a disulfide form the structural framework of proteins
(S-S) bond with another cysteine to form cystine • Protein – long chain of amino acids
PRIMARY STRUCTURE
• Denotes the number and sequence of amino acids in
protein
• Polymerization of amino acids – polypeptide chain
• Each amino acid in the chain is called a residue
Figure 21. Glutathione structure • Structure is linear and linkage is maintained by peptide
bond
A. HOW TO DRAW A PEPTIDE BOND • Higher levels of organization are decided by primary
structure
1. Use a zig-zag to represent the main chain or backbone
à Primary structure determines biologic activity
(HN-CH-C=O). By convention, peptides are written with
à Polypeptide chain has unique amino acid sequence
the residue that bears the free a-amino group at the left. decided by gene sequence as encoded in the genetic
2. Add the main chain atoms: a-nitrogen, a-carbon, carbonyl code
carbon à Gene codes not only determine the order of amino
3. Add a hydrogen atom to each a-carbon and to each acids in a protein, but they also determine a protein's
peptide nitrogen, and an oxygen to the carbonyl carbon structure and function
4. Add the appropriate R groups to each a-carbon atom à When sequence is changed, polypeptide is also
5. Three-letter abbreviations linked by straight lines changed
represent an unambiguous primary structure. Lines are à A single amino acid change (mutation) in a linear
omitted for single letter abbreviations. sequence may have profound effect on the function
• Example: Asp-Ala-Ser à Example in normal hemoglobin (Hb A); amino acid in
B. CHARACTERISTICS OF A PEPTIDE BOND the beta chain – glutamic acid but in sickle cell anemia it
is changed to valine
• It is partial double bond, no freedom of rotation
• It is rigid and planar (O, C, N, and H atoms of a peptide Regular Conformations in Protein
bond are coplanar) • Two broad classes:
• It is trans in nature (except Proline) 1. Globular
à R-groups are on opposite sides of an • Compactly folded and coiled
imaginary reference line on the molecule • For catalytic, regulatory, and transport functions
à Less steric effect from bulk R- groups and 2. Fibrous
less energy needed to maintain structure which
• More filamentous or elongated
makes it more stable
• For structural and contraction functions
• Side chains are free to rotate on either side of peptide
bond
• Peptide Bond has partial double-bond character
2. β- Pleated Sheets
• Composed of two or more of different regions
stretches of at least 5 – 10 amino acids (beta
strands)
• Beta strands are extended polypeptide chains
• Chains are folded so that they lie alongside
each other
• Beta sheet is formed by linking two or more beta
strands by interchain hydrogen bond
• These are pleated due to positioning of the alpha
carbons of peptide bond which alternates above
Figure 22. Secondary Structure of Protein
and below the plane of sheet
• Types of β-pleated Sheet
TYPES OF SECONDARY STRUCTURE à Parallel: adjacent peptide chains proceed in
the same direction
1. a-helix à Antiparallel: adjacent chains are aligned in
• common structure of globular class opposite direction
• Coiled / spiral with rod-like structure
• Tightly coiled backbone forms the inner part of
the rod and side chains extend outward
• Stabilized by intrachain hydrogen bonds
• Carbonyl carbon (CO) of one amino acid forms
H bond with amine nitrogen (NH) of another
amino acid that is situated four residues ahead
in the sequence
• Right-handed alpha helix: more stable
• Favor alpha helix: alanine, aspartic acid,
glutamic acid, leucine, isoleucine, methionine
• Disrupts helix (produces bend): glycine and
proline
• Structures with alpha helix: keratin, collagen,
fibrin
PARTS OF AN a-HELIX STRUCTURE:
• Pitch – the vertical distance in one turn Figure 24. Different b-pleated sheets
o There are 3.6 residues per turn (13 atoms)
• Rise – distance between amino acids SUPERSECONDARY STRUCTURES
• Intermediate in scale between secondary and tertiary
structures.
• Include loops, turns, bends, and other extended
conformational features.
• E.g. structural motifs (repetitive or non-repetitive) such as
the helix-loop-helix motif or the E-F hands of calmodulin.
• Turns and bends
à Short segments of amino acids that join units
of the secondary structure, such as two adjacent
strands of an antiparallel β sheet.
à β turns involves four aminoacyl residues
à Proline and glycine often present in β turns
E. COMPLEX PROTEINS
• Proteins combined with another macromolecule
• Covalently bonded
• 2 types
1. Glycoproteins
• Proteins covalently conjugated with
carbohydrates
• Found in RBC surface, used in blood
typing
2. Lipoproteins
• Associated with storage and transport
of lipids
e.g. high density lipoprotein/ HDL
(good cholesterol) and low density
lipoprotein/LDL (bad cholesterol)