Four levels of protein structure
Simple modelling activities help students to visualise the four levels of protein structure. With this understanding in mind, students research some functions of proteins and discover a curious protein folding computer game called Foldit. Some examples of conserved sequences in DNA coding for protein molecules concludes the activities.
Which parts of protein structures are always the same, shared by all proteins?
Proteins are involved in most processes in the body:
- as enzymes
- as membrane proteins
- as structural proteins.
In which ways are proteins different?
Activity 1 - Building a polypeptide - modelling the work of a ribosome
This video from the Protein Data Bank (PDB) which explains the four levels of structure of a protein, and it also gives excellent illustrations of the functions of different proteins including antibodies and collagen.
Follow the instruction in the Building models of protein structure worksheet to build a range of polypeptides just as a ribosome might do. Answer the questions about protein structure on the sheet.
Activity 2: Building a complex protein in the Foldit game
Watch this six minute introduction to a growing online gaming community solving 3D puzzles and helping biological problems.
Activity 3 Conserved sequences and proteins
Conserved sequences of DNA are pieces of the DNA sequence which are found in more than one species. These sequences are sometimes coding regions and produce chains of amino acids which form common structures in proteins. Conserved sequences are also found in non coding DNA, that used to be called 'junk DNA'. If lots of species have the same sequence of DNA it is very likely to have an important function. One function is thought to be the control of gene expression.
Watch the video Conserved regulatory sequences from Warwick University and answer the questions which follow.
- Why are biologists interested in comparing DNA between trees and small plants?
To try to find the functions of specific regions of DNA
- How do biologists find these conserved sequences?
Genomes of different species are compared using a computer program
- How many gene promoter regions, associated with nucleosomes, have been found conserved in many species?
Thousands of conserved non-coding sequences have been found in promoter regions which switch on and off genes.
- What other types of non-coding sequences are found conserved?
Genes involved in transcription factors and in development of plants
- What is the real value of this research - to identify these conserved regions of DNA?
The value is that it narrows down the regions of the genome which may be useful for research. The team want to study these sequences in more detail.
The details about genes and proteins and Crick's central dogma of one gene one protein have been deliberately left until the genetics topic.
Activity one covers some basic points from the SL topic 2:
This activity also covers the four levels of protein structure also required for HL Proteins
The second and third activities cover rapidly advancing areas of biology. Short videos have been selected to show students a sense of the excitement amongst biologists about the future promise of these new ways of doing biology.
These resources didn't make it into this lesson plan, but could be useful for extension work, or an extended essay.
This is an excellent introduction to the data base on protein structure http://mm.rcsb.org/
This is the Youtube channel for the Protein data bank where there is a great collection of videos
- Tutorial on 1° and 2° structure with 3D molecules
- Great diagrams of secondary structures of proteins
Online three-dimensional molecular models of proteins
- Proteopedia -- Catalase enzymes molecule
- Amylase starts the process of breaking down starch from food into forms the body can use.
- Alcohol dehydrogenase transforms alcohol from beer/wine/liquor into a non-toxic form that the body uses for food.
- Hemoglobin carries oxygen in our blood.
- Fibrin forms a scab to protect cuts as they heal.
- Collagen gives structure and support to our skin, tendons, and even bones.
- Actin is one of the major proteins in our muscles.
- Growth hormone helps regulate the growth of children into adults.
- Potassium channels help send signals through the brain and other nerve cells.
- Insulin regulates the amount of sugar in the blood and is used to treat diabetes.
- Conserved sequences in haemoglobin