Download Biotechnology Unit 3: DNA to Proteins Essential Cell Biology

Biotechnology Unit 3: DNA to Proteins
The Shape and Structure of Proteins
I.
II.
Proteins are by far the most structurally and functionally complex molecules that are known
a. They can range in size from approximately 30 amino acids to more than 10,000 but most are
between 50 and 2,000 amino acids
b. They can be globular, fibrous, filamentous, sheets, rings, spheres, and many other shapes
The shape of a protein is specified by its amino acid sequence
a. There are 20 different amino acids, each with different structural and chemical properties
b. Proteins consist of long chains of covalently bonded amino acids
i. The order of amino acids is called the amino acid sequence and each individual molecule
of a type of protein has an identical amino acid sequence
ii. Bonds are called peptide bonds
iii. Proteins are often called polypeptides
1. The backbone of the protein consists of the repeating amine groups and
carboxylic acid groups of the amino acids and the side chains are the unique
portions of the amino acids
2. These side chains interact with each other or with other chemicals to provide the
structure and function of the protein
c. The protein backbone is very flexible which allows the proteins to fold in an incredible number
of ways
i. Regions of the proteins are held together by noncovalent bonds including hydrogen
bonding, electrostatic connections, and van der Waals attractions
1. Hydrophobic interactions are also very important to protein folding because
several amino acids are nonpolar (hydrophobic) and therefore will be attracted to
each other in aqueous (water based) environments
ii. Each protein will fold into a final shape called a conformation based on its amino acid
sequence
1. Proteins will naturally fold into the lowest possible energy conformation
2. Each protein has one single stable conformation, but there can be slight changes
based on interactions with other molecules
3. Denaturing involves chemically causing the protein to become unfolded (usually
by temperature or pH changes)
4. When proteins fold incorrectly, they can form aggregates that can cause damage
to whole cells or even to tissues
a. Prion disorders like mad-cow disease and CJD in humans
b. Alzheimer’s and Huntington’s disease in humans
iii. The two most common folding patterns are the α-helix (alpha helix) and the β-sheet (beta
sheet)
1. Both of these patterns are common in most proteins and they are both the result of
hydrogen bonds between the backbone molecules and not the side chains
2. An α-helix is caused by a single polypeptide chain turning around itself to form a
cylinder
a. A hydrogen bond forms between every fourth amino acid whit the C=O
of one bonding to the N-H of the other
b. The helix makes a complete turn every 3.6 amino acids
c. Sometimes two or three α-helices wrap around each other to form a
structure called a coiled-coil
3. β-sheets form when hydrogen bonds form between segments of proteins lying
side by side
Essential Cell Biology Chapter 4
III.
IV.
Biotechnology Unit 3: DNA to Proteins
a. Parallel β-sheets are when the polypeptide chains have the same
orientation and antiparallel β-sheets are when they are in opposite
orientations
b. β-sheets have some incredible properties
i. They are what give silk its incredible strength
ii. They are abundant in antifreeze proteins in insects that prevent
them from freezing in extreme cold temperatures
Proteins have several levels of organization
a. The primary structure is the amino acid sequence
b. The secondary structure is the folding of the protein
i. Includes α-helices and β-sheets
c. The tertiary structure involves all of the smaller folds interacting with each other to form the
final structural conformation
d. The quaternary structure is when the protein is combines with other polypeptide molecules to
create a larger structure
e. Proteins also have a level of organization called domains
i. These are units that are usually made up of 100-250 amino acids folded into a secondary
structure that act as modular units that are found in many different types of proteins
ii. Small proteins consist of only one domain where as larger proteins will have several
dozen domains
Protein families consist of groups of proteins that have very similar amino acid sequences and three
dimensional conformations
Essential Cell Biology Chapter 4