1. Chapter 5
Proteins

2. Organic Molecules: Proteins

3. Proteins More than 50% of the dry weight of most cells
Humans have tens of thousands of different proteins, each with a specific structure and function
All proteins are polymers (polypeptides) built from the same 20 amino acids
Used for structural support, storage, transport of substances, signaling from one part of the organisms to another, movement, defense against foreign substances, and as enzymes (see Table 5.1 on Page 72)

4. Proteins Most structurally & functionally diverse group
Function: involved in almost everything
enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication
signals (insulin & other hormones)
receptors
defense (antibodies)
movement (actin & myosin)
storage (bean seed proteins)
Storage: beans (seed proteins)
Movement: muscle fibers
Cell surface proteins: labels that ID cell as self vs. foreign
Antibodies: recognize the labels
ENZYMES!!!!

5. Amino Acids There are only 20 amino acids
Organic molecules possessing both carboxyl and amino groups
Amino acids are grouped according to the properties of their side chains
Some are polar, some nonpolar, some acidic and some basic

6. Nonpolar amino acids - hydrophobic

7. Polar amino acids - hydrophilic

8. Amino Acids
Electrically charged amino acids – side chains are negatively or positively charged causing them to act as acids or bases and to dissociate in water. They are hydrophilic.

9. Peptide Bond
Peptide bond – covalent bond linking amino acids together to form polypeptides
Polypeptides vary in length from a few monomers to thousands or more

10. Proteins
Each specific polypeptide has a unique linear sequence of amino acids
Chains of polypeptides make a protein
A protein’s specific conformation determines how it works
A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape
Four Levels of Structure
Primary, Secondary, Tertiary, Quaternary

11. Protein structure & function
Function depends on structure
3-D structure
twisted, folded, coiled into unique shape
Hemoglobin
Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood.
Pepsin
Pepsin is the first in a series of enzymes in our digestive system that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.
Collagen– Your Most Plentiful Protein
About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein.
pepsin
hemoglobin
collagen

12. Protein Structure
Protein types include globular proteins which are usually enzymes and Fibrous proteins which usually serve for structure (eg. Hair)

13. Primary Structure
The primary structure of a protein is the unique amino acid sequence

14. Primary Structure
A change in the primary structure can affect a protein’s conformation and ability to function

15. Sickle-cell hemoglobin
Primary structure
Secondary and tertiary structures
Quaternary structure
Function
Red blood cell shape
Hemoglobin A
Molecules do not associate with one another, each carries oxygen.
Normal cells are full of individual hemoglobin molecules, each carrying oxygen  
10 m
Hemoglobin S
Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.
 subunit 1 2 3 4 5 6 7
Normal hemoglobin
Sickle-cell hemoglobin
. . .
Figure 5.21
Exposed hydrophobic region
Val
Thr
His
Leu
Pro
Glul
Glu
Fibers of abnormal hemoglobin deform cell into sickle shape.

16. Secondary Structure
Segments of the polypeptide chain repeatedly coiled or folded in unique patters that contribute to the protein’s overall conformation
Results from the hydrogen bonds at regular intervals along the polypeptide backbone, not the amino acid side chains
Can be in the form of an α helix or β pleated sheet

17. Secondary (2°) structure“
-helix
-pleated sheet
It’s a helix or B sheet within a single region. Can have both in one protein but a specific region is one or another

19. Tertiary Structure
Irregular contortions from interactions between side chains of the various amino acids.

20. Quaternary Structure
The association between two or more polypeptides that make up a protein

21. Protein structure (review)
R groups
hydrophobic interactions
disulfide bridges
(H & ionic bonds) 3°
multiple polypeptides
hydrophobic interactions 1°
sequence determines structure and…
structure determines function.
Change the sequence & that changes the structure which changes the function.
amino acid sequence
peptide bonds 4° 2°
determined by DNA
R groups
H bonds

22. What Determines Protein Conformation?
Dependent upon the interactions among the amino acids making up the polypeptide chain
Usually arise spontaneously as soon as the protein is synthesized in the cell
These interactions can be disrupted by changes in pH, salt concentration, temperature, etc. causing the protein to denature, losing its native conformation and thus its function

23. Denaturing of Proteins

24. The Protein-Folding Problem
Chaperonins, chaperone proteins that assist the folding of other proteins.

25. X-Ray Crystallography

26. Review Questions

27. A. What happens when a protein denatures? *
A. What happens when a protein denatures? *
It loses its primary structure.
It loses its secondary and tertiary structure.
It becomes irreversibly insoluble and precipitates.
It hydrolyzes into component amino acids.
Its hydrogen bonds, ionic bonds, and peptide bonds are disrupted.
Answer: All choices are correct, but reflect different levels of conformational change, with Choice B involving the smallest conformational change and Choice D involving the greatest.
Source: Taylor - Student Study Guide for Biology, Sixth Edition, Test Your Knowledge Question #6
Discussion Notes for the Instructor
There are several questions which can be asked to guide the discussion of this question including:
What does “denature” mean? (from glossary denaturation; for proteins, a process in which the protein unravels and loses its native conformation, thereby becoming biologically inactive)
What are the components of a protein?
What are the levels of protein structure?
What type of bonds are involved at each level?

28. B. The R group or side chain of the amino acid serine is –CH2 –OH. The R group or side chain of the amino acid alanine is –CH3. Where would you expect to find these amino acids in globular protein in aqueous solution?
Serine would be in the interior, and alanine would be on the exterior of the globular protein.
Alanine would be in the interior, and serine would be on the exterior of the globular protein.
Both serine and alanine would be in the interior of the globular protein.
Both serine and alanine would be on the exterior of the globular protein.
Both serine and alanine would be in the interior and on the exterior of the globular protein.
Answer: b
Source: Barstow - Test Bank for Biology, Sixth Edition, Question #34