1. Proteins Structurally & functionally diverse group of biomolecules
Function: involved in almost everything
enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
transport (membrane proteins)
defense (antibodies)
movement (actin & myosin)
Storage: beans (seed proteins)
Movement: muscle fibers
Cell surface proteins: labels that ID cell as self vs. foreign
Antibodies: recognize the labels
ENZYMES!!!!

2. Proteins Structure monomer = amino acids polymer = polypeptide
20 different amino acids
polymer = polypeptide
protein can be one or more polypeptide chains folded & bonded together
large & complex molecules
complex 3-D shape
Rubisco = 16 polypeptide chains
Hemoglobin = 4 polypeptide chains (2 alpha, 2 beta)
hemoglobin
Rubisco
growth hormones

3. Amino acids H O | H || —C— C—OH —N— R Structure central carbon
amino group
carboxyl group (acid)
R group (side chain)
variable group
different for each amino acid R

5. dehydration synthesis
Building proteins
Peptide bonds
covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another
C–N bond
H2O
dehydration synthesis
free COOH group on one end is ready to form another peptide bond so they “grow” in one direction from N-terminal to C- terminal
peptide bond

6. 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

7. Primary (1°) structure Order of amino acids in chain
amino acid sequence determined by gene (DNA)
Forming peptide bonds
Sickle cell anemia: 1 DNA letter changes 1 amino acid = serious disease
Hemoglobin mutation: bends red blood cells out of shape & they clog your veins.

8. Secondary (2°) structure
“Local folding”
folding along short sections of polypeptide
interactions between adjacent amino acids
Forming H Bonds
forms sections of 3-D 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

10. Tertiary (3°) structure
“Whole molecule folding”
interactions between distant amino acids
Forming hydrophobic/hydro philic regions
How the whole thing holds together

11. Quaternary (4°) structure
More than one polypeptide chain bonded together
only then does polypeptide become functional protein
Structure equals function wonderfully illustrated by proteins
Collagen is just like rope -- enables your skin to be strong and flexible.
hemoglobin
collagen = skin & tendons

12. Protein structure (review)
R groups 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

13. Enzymes and Chemical Reactions
Unit 1: Biochemistry and Digestion
Enzymes and Chemical Reactions
2.6 Notes

14. What is a chemical reaction?
Bonds are broken, bonds are formed.
 represents a chemical change
Reactants  Products
Chemical Equation
CH4 + 2O2  CO2 + 2H2O
Reactants
4 Hydrogen
1 Carbon
4 Oxygen
Products
4 Hydrogen
1 Carbon
4 Oxygen

15. Enzymes… Are proteins Speed up reactions
Work by lowering activation energy
Are not used up during the reaction
Are specific to one reaction
Have a precisely shaped active site
Active Site

16. Enzyme Vocab Active site Substrate Catalyze/catalyst Product
Enzyme-substrate complex
Active site
Catalyze/catalyst
Activation Energy
Induced fit

17. Enzymes are reused.
Induced fit hypothesis.
Enzymes are reused.

18. Reading an Energy Graph
Unit 1: Biochemistry and Digestion
Reading an Energy Graph

19. Enzymes Lower Activation Energy

20. Activation Energy Analogies
(a) an irritated person who needs only a bit more frustration to explode in anger
(b) small waves that lift debris over a dam
(c) lighting a match around lighter fluid.
In each situation, the output is much greater than the input.

21. Induced Fit Model of Enzyme Function
Unit 1: Biochemistry and Digestion
Induced Fit Model of Enzyme Function

22. Unit 1: Biochemistry and Digestion
Metabolism
Anabolism – building up
Catabolism – breaking down (CATastrophic…)
Exergonic
Releases energy
Energy-rich reactants  Energy-poor products
Endergonic
Absorbs/requires energy
Energy-poor reactants  Energy-rich products

23. Endergonic vs. Exergonic reactions
Unit 1: Biochemistry and Digestion
OBJ 28
Endergonic vs. Exergonic reactions

24. Endergonic vs. Exergonic reactions
Breaking bonds
Building bonds

25. Energy added or released? Endergonic or exergonic?
How does presence of an enzyme change the course of the reaction?

26. What Factors Affect Enzyme Activity?

27. Too Warm = denaturation
1. Temperature
Warmer
Cooler
Too Warm = denaturation

28. 1. Temperature ?
Active Site

29. Temperature vs. Enzyme Activity

30. Other factors affecting enzyme activity
Change Active Site
Change # of Collisions pH
Ion/salt concentration
(Temperature)
Substrate concentration
Enzyme concentration
Pressure
(Temperature)

31. 2. pH and Enzyme Activity
Enzymes may have different optimal pH levels, depending where they need to function.

32. 3. Substrate Concentration
Unit 1: Biochemistry and Digestion
3. Substrate Concentration

33. 4. Enzyme Concentration (with excess substrate)