1. What Are Proteins?
Proteins are large molecules, found in every cell in the plant and made up of chains of amino acids:
Proteins are polymers built through the condensation of amino acids.
The sequence of amino acids is determined by DNA.
Proteins are involved in most of the functions and life processes.
Protein’s molecular weight is from 6000 to several hundred thousand daltons.
Dalton is a unit of mass equivalent to a hydrogen atom,
1 dalton = × 10−27 kg.
Prosthetic groups: organic or inorganic components other than amino acids contained in many proteins.
Conjugated proteins: the proteins contain prosthetic groups.
Proteins are long, unbranched chains (polymers) of smaller biological molecules called amino acids, linked together by a special covalent bond called a peptide bond.
A peptide bond is a covalent bond between an amino group (NH2) of one amino acid and a carboxyl group or acid group (COOH) of a second amino acid. Peptide bonds are formed by dehydration synthesis in a process called translation, which is performed by the ribosomes of the cell.
A peptide bond is formed through condensation and broken through hydrolysis.

2. Basic facts on Amino Acids
Amino acids come in about twenty varieties. (Actually, there are a few more than twenty, and most come in two different stereoisomers, but since the translation process only specifies codes for twenty, those are the most significant in this context.)
All of these amino acids have the same core structure—a carboxyl and an amino group with a single carbon between them—but each has a different R group (or side chain, sometimes called a “residue”) attached to that central carbon.
R groups vary from a simple hydrogen (glycine) to complex ring structures (tryptophan). Some are polar, some non-polar; some are neutral, some acidic, some basic; some are small, some very bulky. As a typical protein might be between 150 and 500 amino acids long, this makes the possible variety in protein behavior very vast.

3. Common structure for Amino AcidsH
COOH
H2N α
COOH, -NH2, H and R functional groups all are attached to the alpha carbon.
Where "R" represents a side chain specific to each amino acid.
Amino acids are usually classified by properties of the side chain into
four groups:
acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar).
α-amino acid are amino acids in which the amino and carboxylate
functionalities are attached to the same carbon, the so-called α–carbon.
They are the building blocks of proteins.

4. The Anatomy of an Amino Acid

6. Condensation and Hydrolytic Reactions

7. Amino Acids Essential – must be consumed in the diet.
Nonessential – can be synthesized in the body.
Conditionally essential – cannot be synthesized due to illness or lack of necessary precursors. Example:
Premature infants lack sufficient enzymes needed to create arginine.
20 common amino acids, others are found naturally but much less frequently.
Essential amino acids: An essential amino acid for an organism is an amino acid that cannot be synthesized by the organism from other available resources, and therefore must be supplied as part of its diet.
Most of the plants and microorganism cells are able to use inorganic compounds to make amino acids necessary for the normal growth.
Eight amino acids are generally regarded as essential for humans: tryptophan, lysine, methionine, phenylalanine, threonine, valine, leucine, isoleucine.
Two others, histidine and arginine are essential only in children. A good tool for remembering these is "Private Tim Hall", abbreviated as:
PVT TIM HALL:
Phenylalanine, Valine, Tryptophan
Threonine, Isoleucine, Methionine
Histidine, Arginine, Lysine, Leucine

8. Standard amino acids

9. limiting amino acid content: the essential amino acid found in the smallest quantity in the foodstuff.
Protein source Limiting amino acid
Wheat lysine
Rice lysine and threonine
Maize lysine and tryptophan
Pulses methionine
Beef methionine and cysteine
Whey none
Milk none

10. Standard amino acids: there are 20 standard amino acids that are commonly found in proteins.

11. Protein Quality Complete proteins
Contain all nine essential amino acids.
Usually animal source are complete proteins and thus are considered higher quality proteins.
Incomplete proteins
Low in one or more essential amino acid.
Usually plant sources are incomplete and are considered lower quality proteins.

12. Proteins: Three-dimensional structure
Two general classes of proteins
Fibrous - long rod-shaped, insoluble proteins. These proteins are strong (high tensile strength).
Globular - compact spherical shaped proteins usually water-soluble. Most hydrophobic amino acids found in the interior away from the water. Nearly all enzymes are globular.
Proteins can be simple - no added groups or modifications, just amino acids
Or proteins can be conjugated- Additional groups covalently bound to the amino acids. The naked protein is called the apoprotein and the added group is the prosthetic group. Together the protein and prosthetic group is called the holoprotein. Example: chlorophyll
Proteins are classified by number of amino acids in a chain
Peptides: fewer than 50 amino acids
Dipeptides: 2 amino acids
Tripeptides: 3 amino acids
Polypeptides: more than 10 amino acids
Proteins: more than 50 amino acids
Typically 100 to 10,000 amino acids linked together.
Proteins vary in size: an average protein probably has between 150 and 500 peptide bonds. For this reason, proteins are often called polypeptides. NOTE that for a protein with quaternary structure (see below) the terms “protein” and “polypeptide” are not interchangeable.

13. Proteins have several layers of organization
Primary (1o) Structure: The primary structure of a protein is the simple amino acid sequence, held together by peptide bonds. The identity and behavior of a protein depends fundamentally upon what amino acids it contains and in what order they are arranged.
Each protein has not only a definite amino acids composition, but also a unique sequence.
The amino acid sequence has profound effect on the resulting three-dimensional structure and on the function of protein.
Secondary (2o) Structure: The secondary structure of a protein consists of a variety of three dimensional configurations which have an organized, symmetrical appearance to the human eye. This level is only concerned with the local or close in interactions in structures on the protein - peptide backbone.
Secondary structures are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule.
Secondary structure occurs as a result of the interactions of the polar bonds in the backbone of a protein, and are therefore due to hydrogen bonding. Not all proteins have secondary structure, and those which do have it vary in the percentage of the amino acid sequence which forms into secondary structure, depending upon a number of structural and sequence features in each protein. Two major kinds of secondary structure are the alpha helix and the beta pleated sheet. Other kinds of molecules also have secondary structure. The famous double helix of DNA is that molecule’s secondary structure.

14. Proteins have several layers of organization
Tertiary (3o) Structure: the tertiary structure of a polypeptide is its total three dimensional structure. It consists of a variety of folding, bending and twisting patterns, many of which make no obvious sense to the eye of human being. However, all of the tertiary structure of a protein is important to its functioning, whether it seems to make sense to the observer or not. And for any particular kind of protein, the tertiary structure will be consistent from molecule to molecule of that protein. Since tertiary structure encompasses all of the three dimensional configuration of protein, it includes the secondary structure. Overall, tertiary structure is produced by a variety of influences which occur between the R groups of the amino acids in the sequences. These influences include hydrogen bonding between polar R groups.
Tertiary Structure is the overall three-dimensional shape that a protein assumes. This includes all of the secondary structures and the side groups as well as any prosthetic groups. This level is also where one looks for native vs. denatured state.
The tertiary structure has a profound effect on a protein’s function.

15. Proteins have several layers of organization
Quaternary (4o) Structure: The quaternary structure of a protein involves the association between two or more polypeptide molecules, or between proteins and non-protein subunits (called cofactors or, if the protein happens to be an enzyme, coenzymes). Cofactors may be inorganic, such as metal ions (minerals) or organic such as heme groups or vitamins. Not all proteins have quaternary structure. Only in the case of protein with quaternary structure the distinction between protein and polypeptide is important. A protein is a complete, functional substance, with all of its parts included; a polypeptide is a single polymer of amino acids, with primary, secondary and tertiary structure. For a protein with quaternary structure the terms “protein” and “polypeptide” are not interchangeable. Example of a protein with quaternary structure is Hemoglobin. Functional hemoglobin is composed of for polypeptide subunits covalently bonded together. Each of the subunits is covalently bonded to an organic cofactor called heme group. A heme group is a porphyrin ring with a metallic cofactor-an iron ion (Fe+3). Hemoglobin, therefore, is an example of all types of quaternary structure. Example of a protein with no quaternary structure is Insulin. Insulin is simply a single, rather short amino acid polymer, with no cofactors of any kind. It has 1o, 2o and 3o structure. But no 4o structure.
This 4o structure has an important role in the control of the catalytic activity of enzymes.
The 3o or 4o structures are usually referred to as "conformations," or “folding” and transitions between them are called conformational changes.

17. Protein α-helix Secondary Structure
Secondary structure: α-helix
- Formed within the same protein chain.
- Hydrogen bonding can occur between
- the α-carboxyl group of one residue and
- the –NH group of its neighbor four units down the same chain.
- The helical structure can be easily disturbed since hydrogen bond is unstable.

18. Protein β-pleated sheet Structure
Secondary structure: β-pleated sheet
- within the same protein molecule
consists of two or more amino acid sequences that are arranged
adjacently and in parallel, but with alternating orientation
-Hydrogen bonds can form between the two strands.
-Hydrogen bonds established between the N-H groups in the backbone of one strand
with the C=O groups in the backbone of the adjacent, parallel strand(s).
- The sheet's stability and structural rigidity and integrity are the result of
multiple such hydrogen bonds arranged in this way.

19. Proteins have several layers of organization

20. Heme group
Conjugated protein: hemoglobin
Prosthetic group: heme in green
Amino acid units in red and yellow

21. Protein 3-D Structure
Proteins are amino acid chains that fold into unique 3-dimensional structures.
The shape into which a protein naturally folds is known as its native state,
which is determined by its sequence of amino acids and interaction of groups.
Any alteration in the structure or sequencing changes the shape and function of the protein

22. Protein Denaturation
Protein Denaturation: A protein that is not in its native state and shape which allows for optimal activity.
Proteins denature when they lose their three-dimensional structure - their chemical conformation and thus their characteristic folded structure.
This change is usually caused by heat, acids, bases, detergents, alcohols, heavy metal salts, reducing agents or certain chemicals such as urea and mechanical agitation.
The proteins can regain their native state when the denaturing influence is removed. Such denature is reversible. Some other denature is irreversible.
Primary structure is unchanged by denaturing.

23. Denaturing a Protein

24. Irreversible egg protein denaturation and loss of solubility,
caused by the high temperature (while cooking it)

25. Summary of Amino Acids and Proteins
Amino acids are basic building blocks of proteins.
They contain acid carboxyl group and base amino group as well as side group R.
They can be neutral, positively or negatively charged.
There are 20 standard amino acids and 10 essential amino acids for human being.
Proteins are amino acid chain linked through peptide bond.
They can be classified into structural protein, catalytic protein, transport protein , regulatory and protective proteins in either globular or fibrous forms.
Attractions and interactions between the side chains cause the proteins to fold into precise three-dimensional shapes
Protein shape determines its function
Proteins are denatured and their shapes changed by heat, acids, bases, detergents, alcohols, heavy metal salts, reducing agents or certain chemicals and mechanical agitation

26. Summary of Amino Acids and Proteins
Protein has three-dimensional structure at four level.
- Primary structure: the sequence of amino acids.
- Secondary structure: a way that the polypeptide chain is extended. α-helix and β-pleated sheet formed by hydrogen bond.
- Tertiary structure: the overall shape of a protein molecule and the result of interaction between R groups mainly through hydrophobic interaction.
- Quaternary: the interaction between different polypeptide chains of protein. This structure is important to the active function of protein especially enzyme.
Protein can be denatured at its three dimensional structure. Protein denature could be reversible or irreversible.