HL IB-Biology 2011/12
#7 STRUCTURE AND FUNCTION OF PROTEINS
7.5 Proteins
Assessment Statements Addressed:
7.5.1 Explain the four levels of protein structure, indicating the significance of each
level.
7.5.2 Outline the difference between fibrous and globular proteins, with reference to two
examples of each protein type.
7.5.3 Explain the significance of polar and non-polar amino acids.
7.5.4 State four functions of proteins, giving a named example of each.
PROTEIN FOLDING
Go to http://biomodel.uah.es/en/model3/index.htm, and on the right panel scroll to ‘4. Proteins.’
Start the tutorial and follow all the links within the protein section. Use the information to
respond to the questions below. Use other sites or your textbook if you need further
clarification or information.
Amino Acids, the building blocks of proteins:
Look at the structure and chemical composition of all 20 amino acids the cell uses to make
proteins.
1. List features that all amino acids share.
2. List features, that distinguish one amino acid from another.
3. Draw the structure of a ‘generic’ amino acid using N for nitrogen, C for carbon, O for
Oxygen, H for hydrogen, and R for residue.
4. Explain the terminology ‘C-terminus’ and ‘N-terminus’ and label each in your drawing of the
amino acid.
Labudda, CHS, 7 Structure Function Proteins.pages
Four levels of protein structure:
Primary Structure
1. Define primary structure.
2. Explain how the primary structure of a protein is determined.
3. Identify the bond(s) that hold together the primary structure.
4. Using the drawing for a generic structure of an amino acid, draw peptide bond between two
amino acids. Label the bond and the C- and N- terminus.
5. Identify the name of the reaction.
1. Define secondary structure.
Secondary Structure
2. Explain how the secondary structure of a protein is determined.
3. Identify the bond(s) that hold together the secondary structure.
4. Identify how many different secondary structures exist and state each by name.
5. Draw the different agreed upon representations for each secondary structure.
Tertiary Structure
Go to http://intro.bio.umb.edu/111-112/111F98Lect/folding.html and watch the simplified animation
of a protein folding into its tertiary structure. The animation is faulty since it does not show
the secondary structure. However, the point is to stress what features about the individual
amino acids drive the folding of the protein. Make sure you read the annotations and rules below
the animation.
1. Define tertiary structure.
2. Explain how the tertiary structure of a protein is determined.
3. Identify the bond(s) that hold together the tertiary structure.
4. Discuss how only 20 amino acids can give rise to an infinite number of different protein
shapes.
STUDYING PROTEIN FOLDING WITH TOOBERS AND TACKS
MEET IN CLASS ON _____________________________
The toober represents the SECONDARY structure of a given protein and the tack represent the
different side chains of amino acids in the protein.
BLUE TACKS:
basic amino acids (+ charge)
RED TACKS:
acidic amino acids (- charge)
YELLOW TACKS: hydrophobic amino acids
WHITE TACKS: polar amino acids
GREEN TACKS: cysteine amino acids
INSTRUCTIONS:
1. Distribute the 15 tacks randomly but evenly along the toober. By doing this, the “tacked
toober” represents a protein made of 15 amino acids.
2. Fold your protein, following the laws of chemistry that drive protein folding:
BASIC LAWS OF CHEMISTRY THAT DRIVE PROTEIN FOLDING
Stably folded proteins simultaneously satisfy several basic laws of chemistry including:
❀ Hydrophobic side chains will be buried on the inside of the globular protein, where they
are hidden from polar water molecules.
❀ Charged side chains will be on the surface of the proteins where they often neutralize
each other and form salt bridges.
❀ Polar side chains will be on the surface of the protein where they can hydrogen bond with
water.
❀ Cysteine side chains often interact with each other to form covalent disulfide bonds that
stabilize protein structure.
• What do you notice when you compare the proteins of different people?
REVERSIBLE DENATURATION:
Many proteins undergo reversible denaturation, by re-folding into their original shape (native
structure) following their complete unfolding (denaturation) by heating.
1. Document your native protein
2. Unfold your protein, then re-fold it based on the same rules of chemistry
3. Check the re-folded protein and compare it with the first time folded protein
REVERSE ENGINEERING
Some of you had problems folding your protein. With 20 amino acids there are many possible
combinations, however, not all exist in nature because not all primary sequences can be folded
into stable proteins. The protein structures we observe are the result of long protein evolution.
Selection acts on the structure of the protein.
1. Fold your protein into a compact globular shape without any tacks
2. Now add the tacks to the folded toober so the folding becomes possible
EFFECT OF MUTATIONS
Some mutations inactivate a protein by destabilizing its native shape.
1. Starting with the “reversed engineered” sequence of tacks from above, mutate one of the
hydrophobic amino acids to a positively charged amino acid
2. What is the effect of that mutation to the protein structure?
3. What mutation will have no or minimal effect on the structure?
5. Define quaternary structure.
Quaternary Structure
1. Explain how the quaternary structure of a protein is determined.
2. Identify the bond(s) that hold together the quaternary structure.
3. State if all proteins have a quaternary structure.
MOLECULAR WORKBENCH SIMULATION
1. Go to: http://workbench.concord.org/database/activities/225.html
2. Launch activity
3. Follow all the steps, answer the questions and print your report at the end
4. Turn in your printed report
TYPES OF PROTEINS AND THEIR ROLE
1. Complete table 1 by describing the function(s) of the listed proteins, then find a few more
examples on your own.
Table 1: Examples of Proteins and Their Function(s)
Protein
Haemoglobin
Actin and Myosin
Insulin
Immunoglobulins
Amylase
2. Define fibrous and globular protein.
3. Compare fibrous and globular proteins.
Function(s)
4. Find examples for each function of proteins listed in table 2 (do not include membrane
proteins). Describe each example you picked in more detail and indicate if the shape is
fibrous or globular.
Table 2: Function and Shape of some Proteins
Function
Structural
Transport
Movement
Defense
Example
Details
Shape