You may have been told proteins are good for you. Do these look good to you?
Proteins as food. To you, these may not look appetizing (or they might), but they do provide a nice supply of amino acids, the building blocks of proteins. Proteins have many important roles, from transporting, signaling, receiving, and catalyzing to storing, defending, and allowing for movement. Where do you get the amino acids needed so your cells can make their own proteins? If you cannot make the amino acids yourself - and some of them you cannot make - then you must eat them.
Proteins are organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and, in some cases, sulfur. Proteins are made of smaller units called amino acids. There are 20 different common amino acids needed to make proteins. All amino acids have the same basic structure, which is shown in Figure below. Only the side chain (labeled R in the figure) differs from one amino acid to another. These side chains can vary in size from just one hydrogen atom in glycine to a large heterocyclic group in tryptophan. The variable side chain gives each amino acid unique properties. The side chains can also characterize the amino acid as (1) nonpolar or hydrophobic, (2) neutral (uncharged) but polar, (3) acidic, with a net negative charge, and (4) basic, with a net positive charge at neutral pH.
Proteins can differ from one another in the number and sequence (order) of amino acids. It is because of the side chains of the amino acids that proteins with different amino acid sequences have different shapes and different chemical properties. Small proteins can contain just a few hundred amino acids. Yeast proteins average 466 amino acids. The largest known proteins are the titins, found in muscle, which are composed from almost 27,000 amino acids.
General Structure of Amino Acids. This model shows the general structure of all amino acids. Only the side chain, R, varies from one amino acid to another. For example, in the amino acid glycine, the side chain is simply hydrogen (H). In glutamic acid, in contrast, the side chain is CH2CH2COOH. Variable side chains give amino acids acids different chemical properties. The order of amino acids, together with the properties of the amino acids, determines the shape of the protein, and the shape of the protein determines the function of the protein. KEY: H = hydrogen, N = nitrogen, C = carbon, O = oxygen, R = variable side chain
Amino acids can bond together through peptide bonds to form short chains called peptides or longer chains called polypeptides (Figure below). A peptide bond is a covalent bond formed from a condensation reaction between two molecules, causing the release of a molecule of water. This bond usually forms between two amino acids, hence forming a peptide or polypeptide. Peptide bonds between amino acids are formed during the process of translation.
Polypeptides may have as few as 40 amino acids or as many as several thousand. A protein consists of one or more polypeptide chains. The sequence of amino acids in a protein’s polypeptide chain(s) determines the overall structure and chemical properties of the protein.
Polypeptide. This polypeptide is a chain made up of many linked amino acids.
The amino acid sequence is the primary structure of a protein. As explained in Figure below, a protein may have up to four levels of structure, from primary to quaternary. The complex structure of a protein allows it to carry out its biological functions.
Secondary structure refers to local sub-structures generated from the primary structure, usually involving alpha helix and beta pleated sheet structures. These secondary structures form through hydrogen bonding between amino acids.
Tertiary structure refers to the three-dimensional structure of a single polypeptide. The alpha-helices and beta-sheets are folded into a compact globule structure. Stability is maintained through hydrogen bonds, disulfide bonds and other interactions.
Quaternary structure is a larger assembly of several polypeptide chains, now referred to as subunits of the protein. The quaternary structure is stabilized by the same interactions as the tertiary structure. Complexes of two or more polypeptides are called multimers. Specifically, a dimer contains two subunits, a trimer contains three subunits, and a tetramer contains four subunits.
Protein Structure. Primary protein structure is the sequence of amino acids in a single polypeptide. Secondary protein structure refers to internal shapes, such as alpha helices and beta pleated sheets, that a single polypeptide takes on due to bonds between atoms in different parts of the polypeptide. Tertiary protein structure is the overall three-dimensional shape of a protein consisting of one polypeptide. Quaternary protein structure is the shape of a protein consisting of two or more polypeptides. For a brief animation of protein structure, see www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf.
The atomic mass of proteins is measured in kilodaltons (kDa). One dalton (Da) is approximately equal to the mass of one proton or one neutron, so a carbon atom has a mass of approximately 12 Da. The molecular weights of amino acids range from 75 Da for glycine to 204 for tryptophan. Human proteins may have molecular weights ranging from a low of about 3.7 kDA to titian, the largest known human protein with 34,350 amino acids and a molecular weight of approximately 3,816.2 kDa.
Functions of Proteins
Proteins are an essential part of all organisms. They play many roles in living things. Certain proteins provide a scaffolding that maintains the shape of cells (structural proteins). Proteins also make up the majority of muscle tissues. Many proteins are enzymes that speed up chemical reactions in cells. Other proteins are antibodies that protect you from pathogens. Antibodies bond to foreign substances in the body and target them for destruction. Still other proteins help carry messages or materials in and out of cells (transport proteins) or around the body. For example, the blood protein hemoglobin (see Figure below) bonds with oxygen and carries it from the lungs to cells throughout the body.
Hemoglobin Molecule. This model represents the protein hemoglobin. The red parts of the molecule contain iron. The iron binds with oxygen molecules.
A short video describing protein function can be viewed at http://www.youtube.com/watch?v=T500B5yTy58 (4:02).
One of the most important traits of proteins, allowing them to carry out these functions, is their ability to bond with other molecules. They can bond with other molecules very specifically and tightly. This ability, in turn, is due to the complex and highly specific structure of protein molecules. The structure-function relationship of proteins is an important principle of biology. A slight difference in the structure of a protein can lead to a difference in the function of that protein, and this can have devastating effects on the cell or organism.
Proteins and Diet
Proteins in the diet are necessary for life. Dietary proteins are broken down into their component amino acids when food is digested. Cells can then use the components to build new proteins. Humans are able to synthesize all but nine of the twenty common amino acids. These nine amino acids, called essential amino acids, must be consumed in foods. Like dietary carbohydrates and lipids, dietary proteins can also be broken down to provide cells with energy. The amino acids regarded as essential for humans are phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, leucine, lysine, and histidine. Additionally, cysteine, tyrosine and arginine are required by infants and growing children.
In addition, certain amino acids (arginine, cysteine, glycine, glutamine, histidine, proline, serine and tyrosine) are considered conditionally essential, meaning they are not normally required in the diet, but must be supplied to specific populations that do not synthesize them in adequate amounts. An example would be with the disease phenylketonuria (PKU). Individuals with PKU must keep their intake of phenylalanine extremely low to prevent mental retardation and other metabolic complications. However, they cannot synthesize tyrosine from phenylalanine, so tyrosine becomes essential in the diet of PKU patients. PKU can be easily detected with a simple blood test. All states in the US require a PKU screening test for all newborns as part of the newborn screening panel. These individuals are placed on a special diet as soon as the disease is detected, a diet that is extremely low in phenylalanine, particularly when the child is growing. The diet must be strictly followed. Those who continue the diet into adulthood have better physical and mental health. Maintaining the diet for life has become the standard recommended by most experts.
- amino acid: Small molecule that is a building block of proteins; the monomer of a polypeptide.
- antibody: A large, Y-shaped protein produced by B cells; recognizes and binds to antigens in a humoral immune response; also known as immunoglobulins (Ig).
- enzyme: Chemical, usually a protein, that speeds up chemical reactions in organisms; a biological catalyst.
- essential amino acid: An amino acid that cannot be synthesized by the organism, and therefore must be supplied in the diet.
- hemoglobin: The iron-containing oxygen-transport protein found in red blood cells; allows oxygen to be transported in the blood.
- kilodalton: 1,000 daltons; a unit that is used for indicating mass on an atomic or molecular scale; a dalton is defined as one twelfth of the mass carbon-12 atom.
- peptide bond: A covalent chemical bond formed between two molecules; usually occurs between amino acids; forms through the release of a molecule of water.
- phenylketonuria (PKU): An autosomal recessive genetic disorder characterized the inability to metabolize the amino acid phenylalanine.
- polypeptide: A chain of amino acids that alone or with other such chains makes up a protein.
- protein: Organic compound made of amino acids.
- structure-function relationship: Principle that states the function of a biological item (molecule, protein, cell) is determined by its structure.
- Proteins are organic compounds that consist of carbon, hydrogen, oxygen, nitrogen, and, in some cases, sulfur. They are made up of repeating units called amino acids. They provide cells with energy, form tissues, speed up chemical reactions throughout the body, and perform many other cellular functions.
Use this resource to answer the questions that follow.
- http://www.hippocampus.org/Biology Biology for AP* Search: Structure and Function of Proteins
- How do amino acids link together?
- What is a polypeptide?
- What does "secondary structure" refer to? Describe examples of secondary structure.
- What causes the tertiary structure to form?
- Describe the hemoglobin protein.
- What is the main difference between active sites and binding sites?
- What is the main role of fibrous proteins?
- Describe collagen.
Additional information can be found at:
- Biomolecules - The Proteins at http://www.wisc-online.com/Objects/ViewObject.aspx?ID=AP13304.
- What is a Protein? at http://learn.genetics.utah.edu/content/begin/dna/.
- What is a protein?
- What determines the primary structure of a protein?
- Describe the structural levels of proteins.
- State three functions of proteins, and explain how the functions depend on the ability of proteins to bind other molecules to them.