What is Protein Structure And Functions ! Biological Sciencess !!

PROTEIN STRUCTURE 

I. Peptide bond – amide bond between alpha-amino and alpha-carboxyl groups of 2 amino acids

A. Chemical properties

1. Peptide bond is polar and planar
(a) electron resonance structure
(b) has partial (40%) double bond character
(c) amide group is planar, usually trans
2. Synthesis
(a) condensation produces water
(b) energy required (ATP hydrolysis)
3. Peptide bond is hydrolyzable
(a) acid hydrolysis generates free amino acids
(i) 6N Hydrochloric acid heated at 110°C for 24 hr in a vacuum
(b) base hydrolysis generates free amino acids
(i) 4N Sodium hydroxide heated at 100°C for 4 hr
 (c) cyanogen bromide cleaves at the COOH-terminal side of Met
 (d) enzymatic hydrolysis of peptide bonds by proteases
(i) peptidases are specific for certain amino acids
 4. Polypeptides are polyampholytes
 (a) ampholyte has both acidic and basic pKa values

 (b) isoelectric point 

pH at which the net charge is zero
For example: H3N+–Ala–Lys–Ala–Ala–COO–
pKa of the Alpha-carboxyl group = 3.6 pKa of the Alpha-amino group = 8.0 pKa of the delta-amino of the Lysine = 10.6 at pH = 1 the net charge is +2 at pH = 6 the net charge is +1 at pH = 14 the net charge is –1
the isoelectric point pI = (pKa2 + pKa3)/2 = (8 +10.6)/2 = 9.3

B. Nomenclature

1. Size
(a) dipeptide (2 aminoacids & 1 peptide bond), tripeptide (3 aminoacids & 2 peptide
bonds)
(b) oligopeptide – several amino acids (up to 20)
(c) polypeptides (more than 20 amino acids). All proteins are polypeptides

II. Physical Forces Governing Protein Conformation

A. Physical forces govern 3-D structure of proteins (Pauling and Corey)

1. bond lengths and angles should be distorted as little as possible
2. structures must follow Van der Waal’s rules for atomic radii
3. peptide bond is planar and trans
4. noncovalent bonding stabilizes structure
 5. conformation can change without breaking bonds (flexibility)

B. Types of non-covalent forces important to protein conformation

1. Hydrophobic forces
(a) hydrophobic residues orient to inside
(b) hydrophilic residues orient out
2. Van der Waal’s potential:
includes electron shell repulsion, dispersion forces, and electrostatic interactions
3. Salt bridges, electrostatic forces
4. Hydrogen bonds

C. Angles of rotation of the polypeptide chain determine structure

1. angles of rotation around alpha-carbon are [y (psi) and j (phi)]
(a) y (psi) is the angle of the alpha-carbon bond to the carbonyl-carbon
(b) j (phi) is the angle of the alpha-carbon bond to the amide-nitrogen
2. primary sequence and angles of rotation for each alpha-carbon completely define
protein conformation
3. only a small number of psi and phi angles are allowed
4. statistical analysis of all proteins yields groups of prefered angles
(a) areas of repeating (psi) and (phi) angles are secondary structures

III. Levels of Protein Structure

A. Primary Structure – amino acid sequence of a polypeptide

1. primary structure determines 3-dimensional structure (Anfinsen)
2. always represented N H 2-terminus to COOH-terminus

B. Secondary structure – regular local conformation of linear segments of the polypeptide chain

1. Secondary structure are stabilized by hydrogen bonds between amide and carbonyl
groups
2. Several types of secondary structure

 (a) alpha-helix

1. right handed helix
2. 3.6 amino acids per turn, rise per helix 5.4 Å, rise per aminoacid 1.5 Å
3. carbonyl oxygen hydrogen bonded to 4th amide hydrogen (nÆn+4)
4. amino acid R-groups orient out
5. proline breaks the helix

(b) beta-pleated sheet

(i) polypeptide chains side by side
(ii) polypeptide chains can be parallel or antiparallel
(iii) carbonyl oxygen hydrogen bonded to amide hydrogen
(iv) beta-strand is a single pass of the polypeptide

(c) reverse turn, beta-bend

(i) allows a sharp turn in polypeptide chain
(ii) carbonyl oxygen hydrogen bonded to 3rd amide hydrogen (nÆn+3)
(iii) Glycine is required

3. Fibrous proteins demonstrate secondary structure
(a) Fibroin
(i) silk is fibroin
(ii) antiparallel-beta-pleated sheet
(b) alpha-Keratin and tropomyosin
(i) alpha-keratins in wool and hair and epidermal layer
(ii) tropomyosin is a thin filament in muscle
(iii) alpha-helix allows elasticity
(iv) alpha-keratin converts to beta-pleated sheet with heat or stretching- disulfides are important to maintenance of keratin secondary structure- alpha-keratins are beta-pleated sheets; feathers and claws

 (c) Collagen
(i) structural protein; skin, bones
(ii) triple helix (not alpha-helix)
(iii) sequence (Gly-Xaa-Pro) ‘ x or (Gly-Xaa-HyPro) x
(iv) glycine required for triple helix to form, contains many modified amino acids
(v) hydroxyproline stabilizes the structure, vitamin C required for hydroxylation;
scurvy

C. Tertiary structure – overall folded conformation of the polypeptide

1. Physical forces affect tertiary structure
(a) Hydrophobic forces - hydrophobic residues orient to inside & hydrophilic orient out
(b) salt bridges, electrostatic forces
(c) Van der Waals radii
(d) Hydrogen bonds
(e) Disulfide bridges

D. Quaternary structure – subunit structure

 1. aggregation of 2 or more subunits
 (a) hetero- or homo- polymers
 2. same forces drive tertiary and quaternary structure
E. Structural elements
1. Sequence motif – small functional linear polypeptide sequence (may not be 3-D)
(a) signal peptide
(b) ER-retention signal
(c) mitochondrial and nuclear targeting signals
(d) RGD cell adhesion motif
2. Supersecondary structure (structural motif)
(a) smallest conformational unit (may be functional)
(b) exam p les àà (helix-loop-helix), hairpin, beta-barrels
- Rossman fold, a nucleotide binding site
- leucine zipper mediates transcription factor dimerization
- zinc finger is a DNA binding motif
 3. Domain
(a) the part of a polypeptide chain that can independently fold into a tertiary structure
(b) often domains have units of function
(c) proteins may contain one or many domains

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