1. Chemical agents PROTEINS: The Molecular Tools of the Cell
Polypeptide Chains: Polymers of amino acids that are arranged in a specific linear sequence and are linked by peptide bonds
Protein: A macromolecule which consists of one or more polypeptide chains folded and coiled into specific conformations.

2. : PROTEINS Are abundant: 50% 0f a cell’s dry weight
Have these important functions:
Structural support
Storage of amino acids
Transport (hemoglobin)
Signaling (chemical messengers)
Cellular response to chemical stimuli (receptor molecules)
Movement (contractile proteins)
Defense against antigens (antibodies)
Catalysis of biochemical reactions (enzymes)

3. MORE PROTEINS:
Vary extensively in structure: Every one has its own unique 3-D shape (conformation)
They are made of only amino acid monomers 20

4. POLYPEPTIDES:
Polymers of amino acids connected in a specific sequence.
AMINO ACIDS:
Building blocks of proteins: consisting of an asymmetric carbon (Alpha Carbon) which is covalently bonded to a
H atom
Carboxyl group
Amino group
Variable (R) Group

5. AMINO ACID:

6. Amino Acid Classification: Those With:
POLAR SIDE GROUPS:
Hydrophilic
Can be uncharged polar or….
Charged polar: These can have…
Acidic side groups (dissociated COOH are Neg.)
Basic side groups (Amino group has an extra H+)
NONPOLAR SIDE GROUPS:
Hydrophobic

7. POLYPEPTIDE CHAINS
Polymers formed when amino acids are joined with PEPTIDE BONDS:
Covalent bonds formed by a condensation reaction that links a COOH of one amino with the Amino Group of the other.
These have polarity
These have a –N-C-C-N-C-C- backbone
Range from a few monomers to a few 1000
Have unique linear sequences

8. PEPTIDE BONDS

9. A Protein’s Function Depends on its Specific Conformation
PROTEIN CONFORMATION: 3 Dimensional Shape of a Protein
NATIVE CONFORMATION: Functional conformation of a protein found under normal biological conditions.

10. CONFORMATIONS:
Enables a protein to recognize/bind specifically to another molecule (hormone/receptor, enzyme/substrate, antibody/antigen)
Caused by a specific linear sequence of amino acids
Is produced when a newly formed polypeptide chain coils and folds spontaneously, mostly due to hydrophobic interactions
Is stabilized by chemical bonds/weak interactions between neighboring regions of the folded protein

11. FOUR LEVELS OF PROTEIN STRUCTURE
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure (2 or more polypeptide chains)

12. PRIMARY STRUCTURE Unique Sequence of Amino Acids in a Protein
Determined by genes
A slight change can affect conformation and function (sickle cell anemia)
Can be sequenced in the lab (Frederick Sanger)

13. SECONDARY STRUCTURE
Regular, repeated coiling and folding of a polypeptide’s backbone (Campbell 5.20)
Contributes to a protein’s overall conformation
Stabilized by H bonds between peptide linkages in the protein’s “backbone” (Carbonyl and amino groups)
Alpha Helices and Beta sheets are the 2 major types

14. SECONDARY: ALPHA HELIX
Secondary Structure: A helical Coil stabilized by H bonding between every fourth peptide bond
Described by Linus Pauling and Robert Corey in ’51
Found in fibrous proteins like keratin and collagen)

15. SECONDARY: BETA (PLEATED) SHEETS
Secondary protein structure which is a sheet of antiparallel chains folded into accordian pleats.
Parallel regions are held together bt interchain or intrachain H bonds between adjacent polypeptides
Make up the dense core of many globular proteins, and a major portion of some fibrous ones

16. TERTIARY STRUCTURE:
The 3 dimensional shape of a protein. The irregular shapes are due to bonding between the side chains and interactions of the side chains and the aqueous environment
Can be weak interactions:
H bonding between side chains
Ionic bonding between side chains
Hydrophobic interactions between nonpolar side chains in protein’s interior

17. TERTIARY STRUCTURE: Can contain covalent linkages:
Disulfide Bridges form between 2 cysteine monomers brought together by the folding of the protein

18. DISULFIDE BRIDGES

19. QUATERNARY STRUCTURE
Structure that results from the interactions between and among several polypeptide chains (Campbell 5.23)
Collagen:Fibrous protein w/3helices supercoiled into a triple helix:VERY STRONG: Animal connective tissue
Hemoglobin: 2 alpha chains, 2 beta chains fit tightly together

20. What Determines Protein Conformation
Influenced by physical and chemical interactions
Can be denatured if:
Transferred to an organic solvent
Chemical agents disrupt H bonds
Chemical agents disrupt ionic bonds
Chemical agents disrupt disulfide bridges
Excessive heat is applied to the protein

21. The Protein Folding Problem:
Hard to predict……..
Most proteins pass through intermediate stages, we can’t always see these, and can’t tell just by looking at the final conformation
The native conformation can be dynamic: alternating between several shapes
CLUES: We can now track a protein through its intermediate stages
CHAPERONE PROTEINS have been discovered which temporarily brace a folding protein