1. Lecture # 6: Proteins & Enzymes
(Chapter 2)
Objectives:
Protein of influenza virus
Antibody
1- Discuss protein structure and functions.
2- Discuss protein denaturation.
3- Explain how enzymes function.

2. Proteins are polymers of aminoacids
The word protein is derived from the Greek word proteios, meaning “of first importance”
Proteins ate the most versatile molecules in the body
Proteins are polymers of aminoacids

3. Aminoacids R Aminoacid Fatty acid
Carboxylic acid group
Amino group
Aminoacid
Fatty acid
They are hydrocarbon chains (R) with an amino group and a carboxylic acid group linked by a central carbon with an hydrogen attached to it
Aminoacids
What makes the difference between different aminoacids is the side chain (R) attached to the central carbon

4. 20 amino acids are used to make all the proteins and they are identical except for the radical (R) group

5. DEHYDRATION SYNTHESIS
Dipeptide Synthesis
DEHYDRATION SYNTHESIS
Dipeptide
H2O +
Peptide bond
Dehydration synthesis creates a peptide bond that joins amino acids

6. Dipeptide Synthesis
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H O H O + N C C N C C H OH H OH R1 R2
Amino acid 1
Amino acid 2
A dipeptide H O H H O + N C C N C C
H2O H OH R1 H R2
(b)
Peptide bond
Dehydration synthesis creates a peptide bond that joins amino acids

7. Peptides named for the number of amino acids:
Dipeptide
Peptide:
It is any molecule composed of two or more amino acids joined by peptide bonds
Peptides named for the number of amino acids:
Dipeptides have 2
Tripeptides have 3
Oligopeptides have fewer than 10 to 15
Polypeptides have more than 15
Proteins have more than 50
A proteins is a large folded chain of more than 50 aminoacids (usually from 50 to 10,000 aminoacids)

8. Protein of influenza virus
Conformation:
It is the unique three dimensional shape of protein crucial to function
Protein of influenza virus
Antibody
The antibody helps disable the virus by binding with it. The antibody is able to carry out this binding because it has a shape that is complementary to that of the virus molecule
Proteins have three to four levels of structural complexity:
1- Primary structure
3- Tertiary structure
2- Secondary structure
4- Quaternary structure

9. Protein Shape Proteins have four levels of structural complexity:
Primary structure
It is the protein’s sequence of aminoacids, which is encoded in the genes.
Secondary structure
It is the arrangement of the aminoacid chain due to hydrogen bonds between atoms at different parts of the chain.
Tertiary structure
It is the complex bending and folding that gives a protein its final tridimensional shape of globular or fibrous shapes.
It is the association between two or more peptide chains to form a protein complex.
Quaternary structure

10. Primary structure
It is the protein’s sequence of aminoacids, which is encoded in the genes.

11. Secondary structure
The way that aminoacid chains are arranged in the space due to hydrogen bonds between the aminoacids next or near to each other d O - d H + d O - d H + d H + O -

12. Tertiary structure
It is the complex bending and folding that gives a protein its final tridimensional shape of globular or fibrous shapes

13. Fibrous proteins:
They form extended sheets or strands. They are tough, durable, and generally insoluble in water. They usually play structural roles

14. Globular proteins:
They are compact, generally rounded, and readily disperse in water forming a colloid

15. Quaternary structure
It is the association between two or more peptide chains to form a protein complex
Antibodies

16. Four Levels of Protein Structure

17. Conformation:
It is the unique three dimensional shape of protein crucial to function
Proteins have the ability to reversibly change their conformation:
Enzyme function
Muscle contraction
Opening and closing of cell membrane pores
Denaturation:
It is the extreme conformational change that destroys function
Extreme heat or pH can denature the proteins

18. Conjugated Proteins:
They are proteins that contain a non-amino acid moiety called a prosthetic group
Hemoglobin contains four complex iron containing rings called a heme moieties
Heme moieties

19. Protein Functions 1- Structure 2- Communication 3- Membrane Transport
keratin – tough structural protein
gives strength to hair, nails, and skin surface
collagen – durable protein contained in deeper layers of skin, bones, cartilage, and teeth
2- Communication
some hormones and other cell-to-cell signals
receptors to which signal molecules bind
ligand – any hormone or molecule that reversibly binds to a protein
3- Membrane Transport
channels in cell membranes that governs what passes through
carrier proteins – transports solute particles to other side of membrane
turn nerve and muscle activity on and off

20. 5- Recognition and Protection
4- Catalysis
enzymes
5- Recognition and Protection
immune recognition
antibodies
clotting proteins
6- Movement
motor proteins - molecules with the ability to change shape repeatedly
7- Cell adhesion
proteins bind cells together
immune cells to bind to cancer cells
keeps tissues from falling apart

21. Enzymes and Metabolism

22. Net energy released by reaction
REACTANTS
PRODUCTS
HYDROLYSIS
ENERGY
Exergonic reaction
PRODUCTS
Glucose + Fructose
Sucrose
REACTANTS
Energy hill
Net energy released by reaction
ENERGY

23. Net energy released by reaction
Most chemical reactions do not occur or occur very slowly spontaneously
Sucrose
REACTANTS
Total released energy
ENERGY
Activation energy
PRODUCTS
Glucose + Fructose
Sucrose
REACTANTS
Activation energy
Net energy released by reaction

24. Activation Energy: The amount of energy required to start a chemical reaction
Many reactions needs a great amount of energy for activation
They have a high activation energy
To provide this amount of energy, the temperature will increase to values that would damage the cells
For example: To digest starch in the laboratory, you must boil it in an acid solution. We could not tolerate these conditions in our body
However, the human organism digest starch with the help of enzymes.

25. SUBSTRATE
High activation energy
1000 C
Enzyme
Lower activation energy
SUBSTRATE
370 C
A B
REACTANTS
SUBSTRATE
PRODUCTS
A + B
Enzymes:
They are proteins that bind to the reactants and lower their activation energy

26. Enzymes and Activation Energy
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Activation
energy
Activation
energy
Net
energy
released by
reaction
Net
energy
released by
reaction
Energy level
Free energy content
of reactants
Energy level
of products
Time
Time
(a) Reaction occurring without a catalyst
(b) Reaction occurring with a catalyst

27. Enzymatic Reaction Steps
The substrate approaches the active site on enzyme molecule 1
Sucrose (substrate) 1
Enzyme and
substrate O
Active site:
Active site
It is the portion of an enzyme that binds with and transforms a substrate
Sucrase (enzyme) 2
The substrate binds to the active site forming the enzyme-substrate complex 2
Enzyme–substrate
complex
This binding is highly specific. The substrate fit a particular enzyme like a lock and key. This selectivity is called enzyme-substrate specificity O
The enzyme breaks the covalent bonds between monomers in substrate by adding H+ and OH- from water (hydrolysis) 3
Glucose
Fructose 3
Enzyme
and reaction
products
The reaction products are released: glucose and fructose
The enzyme remains unchanged and is ready to repeat the process
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

28. One enzyme molecule can consume millions of substrate molecules per minute
The fastest-working enzymes can carry out 100,000 chemical transformations per second, without themselves being changed
Factors that change enzyme shape:
The pH and temperature alters or destroys the ability of the enzyme to bind to substrate.
The enzymes vary in optimum pH:
- salivary amylase works best at pH 7.0
- pepsin works best at pH 2.0
The temperature optimum for all human enzymes is the body temperature (37 degrees C)

29. Cofactors and Coenzymes
They are inorganic substances that are required by some enzymes
They bind to enzyme and induces a change in its shape, which activates the active site, which is essential to function
About 2/3rds of human enzymes require a nonprotein cofactor
Some cofactors are iron, copper, zinc, magnesium and calcium ions
Coenzymes:
They are organic cofactors that facilitate the work of the enzymes. Many coenzymes are derived from water-soluble vitamins (niacin, riboflavin)
Riboflavin
Niacin
They accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another

30. Metabolic Pathway:
It is a chain of reactions, with each step usually catalyzed by a different enzyme
Enzyme 1
Enzyme 2
Enzyme 1
Enzyme 2
Coenzyme
Coenzymes accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another

31. A B C D Metabolic Pathway:
It is a chain of reactions, with each step usually catalyzed by a different enzyme.
Intermediates A B C D
Initial reactant
Product
Enzyme 1
Enzyme 2
Enzyme 3
A is initial reactant, B+C are intermediates and D is the end product.
Enzyme 1
Enzyme 2
Enzyme 3
Intermediates