Prof.
Minda Aquino
MC 2 Biochemistry
https://www.livescience.com/
3505-chemistry-life-human-
body.html
MODULE 4
Bioorganic Compounds: Proteins and Enzymes
Title: Module 4
Bioorganic Compounds: Proteins
Overview:
Proteins are one of the most abundant organic molecules in living systems and have the
most diverse range of functions of all macromolecules. Proteins may be structural, regulatory,
contractile, or protective; they may serve in transport, storage, or membranes; or they may be
toxins or enzymes. Each cell in a living system may contain thousands of different proteins,
each with a unique function. Their structures, like their functions, vary greatly. They are all,
however, polymers of alpha amino acids, arranged in a linear sequence and connected together
by covalent bonds. (https://wou.edu/chemistry/courses/online-chemistry-textbooks/ch450-and-
ch451-biochemistry-defining-life-at-the-molecular-level/chapter-2-protein-structure/)
Learning Outcome:
1. Describe and classify proteins based on their: characteristics, functions, compositions,
structure
2. Name and classify amino acid based on: the structural differences of its side chain
(nonpolar, polar uncharged, acidic, basic) capacity of the body to synthesize each.
3. Describe the chemical nature of enzymes.
4. Explain the six classes of enzymes based on the types of chemical reactions they
catalyze.
5. Explain the factors that affect enzyme activity.
Objectives:
At the end of the module the students shall be able to:
1. Define proteins and enzymes;
2. Classify proteins according to functions and structure;
3. Define amino acids and identify its characteristics;
4. Identify amino acids commonly found in proteins and its classification;
5. Enumerate 6 major groups of enzymes;
6. Identify factors that influence enzyme activity;
7. Identify chemistry connection among humans.
Reference:
Bettelheim, F.A., Brown, W.H., and Campbell, M.K. () Introduction to Organic and Biochemistry,
6th ed.,
**images taken from google
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PROTEINS
- Proteins are the most complex and important biological compounds and food
substances. They are made up of amino acids that are linked together by a peptide
bond.
- Proteins perform variety of functions:
1. STRUCTURAL – are proteins which are the chief constituents of skin, bones, hair,
and nails. The two important structural proteins are collagen and keratin.
2. CATALYSTS – enzymes, without enzymes reactions would take place slowly.
3. MOVEMENT – proteins are involved in body movement thru muscular contraction.
Muscles are made up of protein molecules called myosin and actin.
4. TRANSPORT – they also perform transportation across cell membranes. Example,
hemoglobin carries O2 from the lungs to the cells and CO2 from the cells to the lungs
during respiration.
5. HORMONES – like insulin, growth hormone, erythropoietin and human growth
hormone.
6. PROTECTION – protein can protect the body when outside source of protein called
antigens enter the body, they induced the production of antibodies that can be used
to fight diseases.
- Blood clotting is another protective function carried out by a protein (fibrinogen);
when fibrin threads are formed during clot formation.
7. STORAGE – some proteins store materials like casein in milk, ovalbumin in egg,
ferritin in the liver that can store iron.
8. REGULATION – some proteins can control the expression of genes and can
regulate the kind of proteins that can be synthesized in a particular cell.
- Clearly, individuals need a great variety of proteins. The entire human
body has about 100,000 different kinds of proteins.
- Proteins can be classified into two major types, the fibrous and the
globular proteins.
- If the end product of metabolism of carbohydrates are in the form of
simple sugar and lipids as fatty acid, proteins can be absorbed as amino
acids.
- Proteins are classified into major classes
1. FIBROUS PROTEINS – are insoluble in water and are used mainly for structural
purposes.
2. GLOBULAR PROTEINS – are less soluble in water and are used mainly for
nonstructural purposes.
Proteins – made up of large molecules of polypeptides that are link together by monomers.
Proteins degradation proteoses/peptones degradation polypeptides
Amino acids degradation Tripeptide/dipeptide degradation
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What are Amino Acids?
- Amino acids are organic compounds containing a carboxyl group (COOH) and an amino
group (NH2).
- The amino acids are classified as:
A. Essential – are those that are obtain from our diets because they cannot be synthesize
in our body, these are:
Valine Lysine
Leucine Arginine
Isoleucine Phenylalanine
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Threonine Histidine
Methionine Tryptophan
B. Non-essential – those amino acids which can be synthesized in our body. And these are:
Glycine Glutamate
Alanine Aspargine
Serine Tyrosine
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Cysteine Proline
Aspartate Glutamine
- The most important aspect of amino acids is their polarity. On that basis, they can be
further classified as:
1. Non polar are amino acids that are hydrophobic (they repel water)
2. Polar but neutral, acidic, basic (attract water) hence they are called hydrophilic.
20 AMINO ACIDS COMMONLY FOUND IN PROTEINS
NAME STRUCTURE CLASSIFICATION
1. Alanine Non polar
2. Arginine Basic
3. Aspargine Polar uncharged
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4. Aspartic Acid Acidic
5. Cysteine Acidic
6. Glutamic Acid Acidic
7. Glutamine Polar uncharged
8. Glycine Polar uncharged
9. Histidine Acidic
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10. Isoleucine Acidic
11. Leucine Non-polar
12. Lysine Basic
13. Methionine Acidic
14. Phenylalanine Acidic
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15. Proline Non-polar
16. Serine Polar uncharged
17. Threonine Acidic
18. Tryptophan Acidic
19. Tyrosine Acidic
20. Valine Non-polar
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What are Zwitterions?
- Are compounds having a positive (+) charge on one atom and a negative (-) charge on
another. This came from a German word zwitter which means hybrid. Amino Acids are
zwitterions not only in water but also in the solid state.
How do amino acids combine to form proteins?
- Each amino acid has a carboxyl group and an amino acid group to form an amide. This
reaction takes place in the cells by a mechanism, the product is an amide. The two
amino acids joined by a peptide bond, called peptide linkage, the product of which is a
dipeptide.
- Equation:
Glycine + alanine Glycylalanine (peptide)
- When 2 amino acids combine, a dipeptide is form.
CHEMICAL CONNECTION: AGE and AGING
• A reaction can take place between a primary amine and an aldehyde or a ketone linking the
two molecules.
•
•Since protein has NH2 group and carbohydrates have CHO or CO group, they undergo the
reaction establishing a link between a sugar and a protein molecule, when this reaction is not
catalyzed by enzyme, it is called glycation of proteins.
• The process does not stop there. When these products are heated, water insoluble, brownish
complexes form. These complexes are called advanced glycation end-products (AGE).
• The longer we live, and the higher the blood sugar concentration becomes, the more AGE
products accumulate in the body. AGE products the accumulate in the body contribute to,
• Joint and vision problems in people with diabetes;
• Eye cataracts and in the capillary blood vessels of the retina, diabetic retinopathy and in the
glomeruli of the kidneys (kidney failure).
• AGE is also linked to atherosclerosis or can bind to endothelial cells in blood vessels, as
modified collagen causing the stiffening of arteries.
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CHEMICAL CONNECTION: GLUTATHIONE
• Is a tripeptide present in high concentration in all tissues. It contain glutamic acid + cysteine +
glycine.
• It functions in the cells as a general protective agent. Oxidizing agents such as peroxide and
many foreign chemicals, would damage the cells and become bonded to glutathione and
become a detoxifying agent.
ENZYMES
- Are chemical secretions coming from cells in our body. They act as catalyzers to hasten
and increase the rate of a chemical reaction.
- Majority of known proteins are globular proteins. Example, ribozymes are enzymes
made up of ribonucleic acids.
- Enzymes are distributed according to the body need to catalyze specific reactions.
Example. Digestive enzymes – stomach/pancreas
SIX MAJOR GROUPS OF ENZYMES
1. Oxiporeductases – catalyze oxidations and reductions
Example. Lactate dehydrogenase
2. Transferases – catalyze transfer of a group of atoms from one molecule to another.
3. Hydrolases – catalyzes hydrolysis reactions
4. Lyases – catalyzes the addition of two groups to a double bond
5. Isomerases – catalyze isomerization reactions
6. Ligases – catalyzes the joining of two molecules
FACTORS THAT INFLUENCE ENZYME ACTIVITY
1. Enzyme and substrate concentration
- Constant substrate concentration increases concentration of enzyme; rate
increases. If doubled, rate also double.
2. Temperature
- In uncatalyzed reaction, rate usually increases as temperature increases.
- Example. Bacterial action – 37oC
Organism ocean floor – 2oC
3. pH – enzymes operates best at a certain pH.
ENZYME MECHANISM
Lock and Key Theory
- explain the specificity of enzyme action by comparing the active site to a lock and the
substrate to a key.
- This theory assumes that the enzyme is a rigid that contain the active site that is
restricted to an opening; which only one kind of substrate can fit.
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- According to the lock and key model, an enzyme molecule has its particular shape
because the shape is necessary to maintain the active site in exactly the same
conformation required for that particular reaction.
Induced-Fit Model
- Explain the phenomenon of competitive inhibition. The inhibitor molecule fits into the
active site cavity in the same way the substrate does.
Now, click the link and watch some videos related to the
topic.
Protein
https://www.youtube.com/watch?v=AUMJwjLXh1M
Protein
https://www.youtube.com/watch?v=HSCUAjZQhXI
Protein - Structure Of Protein - What Is Protein Made Of -
Structure Of Amino Acids Building Blocks
https://www.youtube.com/watch?v=Gi9A56nu01E&t=193s
Enzymes
https://www.youtube.com/watch?v=qgVFkRn8f10&t=1s
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