Monday, October 20, 2008

5.4-Proteins have many structures

Proteins-Many Structures, Many Functions

Proteins are a very important component of the cell; in fact, they make up about 50% of the cell.

*Proteins are polymers made up of amino acid monomers

*The most important type of proteins are enzymes; enzymes regulate metabolism by acting as catalysts(chemical agents that selectively speed up chemical reactions in the cell)

*Proteins consist of one or more polypeptides folded and coiled into specific conformations

Amino Acids are organic molecules that contain a carboxyl group and an amino group, as well as an R group (Variable Group), that gives each amino acid its identity and property. There are 20 amino acids that make up protein molecules. You should be able to recognize from their names that they are amino acids, because most amino acids end in –ine. Ex: Glycine, Glutamine

*The physical and chemical properties of the side chains determine the charctersitics of the Amino Acid

*Acidic Amino Acids have amino groups in their side chains that are negative in charge

*Basic Amino Acids have amino groups in their side chains that are positive in charge

*When 2 Amino Acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, an enzyme can cause them to join by catalyzing a dehydration reaction.

The chain with the amino end is called the N- Terminus, and the carboxyl end is called the C-terminus.

*In proteins, amino acids are joined by peptide bonds in a dehydration synthesis reaction. The function of proteins depends on how many amino acids and what type of amino acids are joined together.

Protein Conformation and Function

*There are four levels of protein structure. We can recognize three superimposed levels of structure, known as primary, secondary, and tertiary structure. The fourth

level, quaternary structure, arises when a protein consists of 2 or more polpeptide chain

The Primary Structure:

·This structure is the protein’s unique sequence of amino acids.

· The precise primary structure of a protein is determined not by the random linking of amino acids, but by inherited genetic information

The Secondary Structure:

* Refers to one of the two three-dimensional shapes that the protein can have due to its hydrogen bonding. One shape is a coiled shape called an alpha helix, and the second shape is an accordion shape called a beta pleated shape.

~ Alpha Helix Ex: Hair

~ Beta Pleated Sheet Ex: Silk protein of a spider’s web

* These coils and folds are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone.

*Both the oxygen and the nitrogen atoms of the backbone are electronegative, with partial negative charges

The Tertiary Structure:

· Refers to interactions between side chains of the protein. These interactions involve hydrophobic interactions, Van der Waals forces, and disulfide bridges.

- As a polypeptide folds into its functional conformation, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact with water.

·Van der Waals forces, disulfide bridges and hydrophobic interactions can all occur in one protein

The Quaternary Structure

· Refers to the association of 2 or more polypeptide chains into one giant macromolecule, or functional protein.

·Ex: Collagen, a fibrous protein that has helical subunits intertwined into a larger triple helix, giving the long fibers great strength.

· Ex: Hemoglobin, consists of 4 polypeptide subunits, two of alpha helix, and two of beta pleated


· When a protein is denatured, upon heating or the introduction of a pH change or other disturbance, it becomes inactive. Denaturation causes the protein to lose its shape, or conformation.

· Most proteins become denatured if they are transferred from an aqueous environment to an organic solvent, such as ether or chloroform

· Other denaturation agents include chemicals that disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain a protein’s shape.

·When a protein in a test-tube solution has been denatured by heat or chemicals, it will often return to its functional shape when the denaturing agent is removed. However, in the crowded environment inside a cell, correct folding may be more of a problem than it is in a test tube.

Nucleic Acids-Informational Polymers

· The last group of important biological molecules we’ll discuss is the nucleic acids. The two Nucleic Acids are DNA (deoxyribonucleic Acid) and RNA ( Ribonucleic Acid)

· DNA is the molecule of heredity. It is what is inherited from cell to cell, parent organism to offspring. DNA molecules are very long; they are polymers of nucleotide monomers. Nucleotides are made up of three parts: a nitrogenous base, a five carbon sugar called pentose, and a phosphate group.

· Each gene along the length of a DNA molecule directs the synthesis of a type of RNA called messenger RNA (mRNA). The mRNA molecule then interacts with the cell’s protein-synthesizing machinery to direct the production of a polypeptide.

· There are two types of nitrogenous bases, purines and pyrimidines. The purines are adenine, abbreviated A, and Guanine (G), and the pyrimidines are cytosine (C), thymine (T) and uracil (U).

· A pyrimidine has a six-membered ring of carbon and nitrogen atoms

· Purines are larger, with a six-membered ring fused to a five-membered ring.

· Thymine is found only in DNA, and Uracil is found only in RNA. In DNA, adenine always pairs with thymine, and cytosine always pairs with guanine.

Multiple Choice Questions:

1. All of the following are found in the strructure of an Amino Acid, except:

A) Amino Group

B) Carboxyl Group

C) Phosphate Group

D) Hydrogen Atom

E) Variable Group, R

2. Which of the following correctly describes the primary structure of a protein?

A) There is a random linking of amino acids

B) The pattern of amino acids is the same for every protein

C) There are always 15 amino acids in a protein

D) The precise primary structure is determined by inherited genetic information

3. All of the following can lead to the denaturing of a protein, except

A) Extreme heat

B) Sudden change in environment

C) Certain Chemicals

D) Interaction with other proteins

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