MolBio_Sp04_pres_08

Transport & storage of small molecules (O2 transport by hemoglobin) Transmitting Information between cells (e.g., hormones)
2.
3.
4.
5.
Defense against infection (e.g., antibodies)

Covalent disulfide bonds between the sulfhydryl groups of Cys residues stabilize folded structures of many proteins
Zinc fingers
Contain repeats of cysteine & histidine • Bind zinc ions • Fold into looped structures
Proteins
Primary functional molecules of the cell; execute the tasks directed by the genetic material
1.
Structural molecules (e.g., hair, fingernails, connective tissue)
Sheet (ribbons)
Models of -sheet 2.20
Turn

Reverses the direction of the chain
X
Pro
Gly
Tertiary Structure

3D arrangements of secondary structure Folding is result of interactions between side chains of a.a. that lie in different regions of the primary sequence Domains: basic units of tertiary structure
2.
3.
4.
Protein Structure

Determines function Folding is defined by 2 parameters
1.
2.
Properties of R-groups
Bond angles about Ca

Folded shape is called conformation
Helix-loop-helix 6.27
•Contain DNA-binding domains formed by dimerization of two polypeptide chains
•Dimerization domains are each formed by two helical regions separated by a loop

3D folding stabilized by disulfides For secreted proteins (mostly) Covalent linkage between cysteines
Important structures in transcription factors
Helix-turn-helix
•One helix makes most of the contacts with DNA, while the other helices lie across the complex to stabilize the interaction.
QuaternHale Waihona Puke ry Structure 2.21


3D arrangement of subunits (different polypeptide chains interacting together) Example: Hemoglobin 4 Subunits Arrangement controls O2 affinity
Special Importance of Some A.A.
1.
Glycine: provides the most flexibility to backbone bond rotation Histidine: complexes with inorganics such as zinc & iron; can be uncharged or (+) charged, therefore involved in ion exchange reactions Proline: only a.a. that is 2ndary amine, severely constrains peptide bond, will break alpha-helical structure Cysteine: thiol groups is most chemically reactive modification of all a.a. in protein, complexes with inorganics such as zinc & iron
Basic & Acidic Amino Acids 2.14
Lysine & Arginine are very positively charged in the cell (hydrophilic) Histidine can be uncharged or positively charged (involved in ion exchange)
Protein Folding

Folding controlled by weak forces Fully folded called native state Unfolded called denatured state
Covalent (disulfide) Bonds 2.16
1. H atom 2. Amino group (NH3+) 3. Carboxyl group (COO-)
4. R group (side chain)
R-group (Side Chain)

R -group determines identity, function

A.A. are categorize by chemical properties of the side chains
Enzymes (catalyze nearly all biochemical reactions)
Amino acids 2.13

20 different amino acids in proteins
Chemical properties of side chains determine function Central carbon atom (Ca)
Uncharged and Polar Amino Acids 2.14
Hydroxyl groups
Amide groups
Polar side chains can form H bonds with water; therefore, are hydrophilic & tend to be located on the outside of proteins
Four Levels of Structure
1) Primary

sequence of amino acids
2) Secondary

regular repeating local structures
3) Tertiary

3D folding
4) Quaternary

3D arrangement of subunits
“Flexibility” at Ca
Peptide bond configuration
The peptide bond nearly always has the trans configuration since it is more favorable than cis, which is sometimes found to occur with proline residues

Defines amino (N) terminus and carboxy (C) terminus
Peptide Bond Resonance
Bond between the carbonyl carbon and the nitrogen has a partial double bond character; therefore, rotation around this bond is restricted
Secondary Structures
Two main types: a helix sheet
Two minor types: Random coil turn
a helix

Regular right handed helix 3.6 amino acids per turn Regular H-bonding (backbone) R groups displayed to exterior Many are amphipathic


Independently folded Often function independently Proteins built in „modules‟ that are strung together