Chapter 4 biochemitry

8/12/2019 Chapter 4 biochemitry

1/27


2/27

Terminology

Conformation spatial arrangementof atoms in a protein

Native conformation conformationof functional protein


3/27


4/27


5/27


6/27

Protein Classification Simple composed only of amino acid residues

Conjugated contain prosthetic groups

(metal ions, co-factors, lipids, carbohydrates)Example: Hemoglobin Heme


7/27

Protein Classification One polypeptide chain - monomeric protein

More than one - multimeric protein

Homomultimer- one kind of chain

Heteromultimer- two or more differentchains

(e.g. Hemoglobin is a heterotetramer. It hastwo alpha chains and two beta chains.)


8/27

Protein ClassificationFibrous 1) polypeptides arranged in long strands or

sheets2) water insoluble (lots of hydrophobic AAs)3) strong but flexible

4) Structural (keratin, collagen)

Globular

1) polypeptide chains folded into spherical orglobular form2) water soluble3) contain several types of secondary structure4) diverse functions (enzymes, regulatory

proteins)


9/27

keratin

collagen

catalase


10/27

Protein Function

Catalysis enzymes

Structural keratin

Transport hemoglobin

Trans-membrane transport Na+/K+ ATPases Toxins rattle snake venom, ricin

Contractile function actin, myosin

Hormones insulin

Storage Proteins seeds and eggs Defensive proteins antibodies


11/27

4 Levels of Protein Structure


12/27

Non-covalent forcesimportant in determining

protein structure

van der Waals: 0.4 - 4 kJ/mol hydrogen bonds: 12-30 kJ/mol

ionic bonds: 20 kJ/mol

hydrophobic interactions:


13/27

1oStructure Determines 2o, 3o, 4oStructure

Sickle Cell Anemia single aminoacid change in hemoglobin related todisease

Osteoarthritis single amino acidchange in collagen protein causesjoint damage


14/27

Classes of 2oStructure

Alpha helix

B-sheet

Loops and turns


15/27

2oStructure Related to Peptide Backbone

Double bond nature of peptidebond cause planar geometry

Free rotation at N - aC and aC-carbonyl C bonds

Angle about the C(alpha)-N bondis denoted phi (f)

Angle about the C(alpha)-C bond is

denoted psi (y)

The entire path of the peptidebackbone is known if all phi and psiangles are specified


16/27

Not all f/yangles are possible


17/27

Ramachandran Plots

Describes acceptable f/yangles for individualAAs in a polypeptide chain.

Helps determine what types of 2ostructure

are present


18/27

Alpha-Helix

First proposed by Linus Pauling andRobert Corey in 1951

Identified in keratin by Max Perutz A ubiquitous component of proteins

Stabilized by H-bonds


19/27

Alpha-HelixResidues per

turn: 3.6

Rise per residue:1.5 Angstroms

Rise per turn(pitch): 3.6 x 1.5A= 5.4 Angstroms

amino hydrogen

H-bonds withcarbonyl oxygenlocated 4 AAsaway forms 13atom loop

Right handedhelix


20/27

Alpha-Helix

All H-bonds in thealpha-helix areoriented in thesame directiongiving the helix adipole with the N-terminus being

positive and theC-terminus beingnegative


21/27

Alpha-Helix

Side chain groupspoint outwards fromthe helix

AAs with bulky side

chains less common inalpha-helix

Glycine and prolinedestabilizes alpha-

helix


22/27

Amphipathic Alpha-Helices

+

One side of the helix (dark) has mostly hydrophobicAAsTwo amphipathic helices can associate throughhydrophobic interactions


23/27

Beta-Strands and Beta-Sheets Also first postulated by Pauling and

Corey, 1951 Strands may be parallel or antiparallel

Rise per residue: 3.47 Angstroms for antiparallelstrands

3.25 Angstroms for parallel strands

Each strand of a beta sheet may bepictured as a helix with two residuesper turn


24/27

Beta-Sheets

Beta-sheetsformed frommultiple side-by-side beta-strands.

Can be in parallelor anti-parallelconfiguration

Anti-parallel beta-sheets more stable


25/27

Beta-Sheets Side chains point alternately above and below the

plane of the beta-sheet 2- to 15 beta-strands/beta-sheet

Each strand made of ~ 6 amino acids


26/27

Loops and turns

Loops

Loops usually contain hydrophillic

residues. Found on surfaces of proteins

Connect alpha-helices and beta-sheets

Turns Loops with < 5 AAs are called turns

Beta-turns are common


27/27

Beta-turns allows the peptide chain to reverse direction

carbonyl C of one residue is H-bonded to theamide proton of a residue three residues away

proline and glycine are prevalent in beta turns

Documents

Chapter 4 biochemitry