Unit 2 - Topic 2.1 Learning Objectives
● Discuss the structural and functional features of biological membranes, and relate how the different macromolecular components (lipids, proteins, carbohydrates) interact to form biological membranes● Describe the chemical properties of phospholipids, cholesterol and glycolipids, and know how these properties contribute to the lipid bilayer structure and function ● Recognize the 20 amino acids according to their chemical properties and their 3-letter and 1-letter abbreviations● Differentiate between the primary, secondary, tertiary, and quaternary levels of protein structure● List and discuss the role of non-covalent bonds in protein folding and stabilization of protein structure● Illustrate how the primary sequence and the environment of a protein influence its final 3D structure
Unit 2 - Topic 2.2 Learning Objectives
● Describe factors affecting or regulating the fluidity of the lipid bilayer● Predict the relative fluidity of membrane bilayers based on their lipid composition● Explain how Fluorescence Recovery After Photobleaching (FRAP) works and interpret results of FRAP experiments ● Describe membrane asymmetry and explain the origin of the asymmetric distribution of membrane lipids
Unit 2 - Topic 2.3 Learning Objectives
● Distinguish between integral and peripheral proteins with regard to their solubility properties, structure and manner of attachment to membranes● Describe the techniques used to study membrane proteins:a) Bioinformatics approach to predict transmembrane domains in proteins (e.g. Hydropathy plots)b) Biochemical approaches to determine membrane protein type, components, and orientation (e.g. SDS-PAGE, fluorescence staining, carbohydrate staining for glycoproteins)● Interpret results from SDS-PAGE, fluorescence and glycoprotein staining experiment sot determine orientation and location of proteins and glycoproteins in a membrane● Predict the hydropathy profile for a given protein given its primary amino acid sequence, or for a given hydropathy plot, predict the amino acid composition of the protein domains within a membrane protein.
Unit 2 - CONTENT REVIEW QUESTIONS:
Topic 2.1 – Review of the Features of Biological Membranes
Lipid Questions
a) Find images of the following molecules in your textbook or online (2). a. 2 different phospholipids of your choice. Take note of their names. What do their names tell you about them? b. Cholesterol (for an extra challenge find an equivalent plant sterol) c. A glycolipid of your choice (for an extra challenge, find 2) d. Sodium dodecyl sulfate (SDS, a detergent)Examine the molecular structures and label the following regions (note that they may not all exist in all of the molecules): • The polar region (differentiate between charged and uncharged molecules of the polar region) and the non-polar region • A region that would be stiff and inflexible • A glycerol residue (some molecules have a serine residue instead, does yours?) • A region that could easily have C=C bonds added (how would that effect the structure of that region?)b) For the molecules you found above, identify which ones would be able to form lipid bilayers on their own. Use the details of the structures to explain why or why not. (2)Protein Questions
a) Define the four levels of protein folding and explain how each one is stabilized (1).b) Self-assembly of macromolecules is an important concept. What do you think that means? What is its relation to denaturation and renaturation? (2)c) What about disulfide bridges? Are they covalent or non-covalent interactions? How do they form? Why are they considered to be uncommon in the cytosol? (2).d) Find images of all 20 amino acids (don’t memorize them!) online or in your textbook. Critically assess the structures, and identify the following (3): • The portion of the amino acid that is common to all of them. • The portion that is unique to each amino acid, known as the R-group or side-chain. • The functional groups that will form the peptide bond. Will anything be lost/ gained during that reaction? How do these parts relate to the ‘N’ and ‘C’ terminus of a protein? • The next questions are specifically for the R-groups. Based solely on their structure, identify the following:
- Any R-groups that you would expect to have ACIDIC properties. Will they gain or lose a proton during that reaction?
- Any R-groups that you would expect to have BASIC properties. Will they gain or lose a proton during that reaction?
- Any R-groups that would not be able to form H-bonds with water
- R-groups that would form H-bonds but would not be acidic or basic.
- R-groups that could interact ionically with their neighbours?
- Any R-groups you would consider to be ‘big’ or ‘small’ relative to the others?
e) Compare what you’ve learned during this structural analysis of the R-groups to how they are categorized by your textbook and try to justify those categories to yourself. Make sure you know the 1- and 3-letter codes for each amino acid (2).Topic 2.2 – The Lipid Bilayer
a) What are the major differences between a synthetic phospholipid bilayer and a biological membrane? (2)b) How do cells adjust to maintain fluidity of their lipid bilayers in varying conditions? (1)c) Despite appearances, cholesterol cannot form bilayers on its own. Use the structure of the molecule to explain why. (3)d) Explain how the structure of phospholipids is the basis of the major properties of the bilayers that they form: physical form of the bilayer, self-sealing property, selective permeability, and fluidity of the bilayer. (3)e) Why are lateral movements of phospholipids in a bilayer so much easier than 'flips' from one leaflet to the other? Explain why this means that we sometimes call a biological membrane a 'two-dimensional fluid' (2)Topic 2.3 – Membrane Proteins
a) What is the difference between integral and peripheral membrane proteins? Discuss and compare the different strategies for association of proteins with membranes. (1)b) What is a domain in a protein? How does it relate to structure and/ or function? (2)c) Compare the hydrophobic forces that hold a membrane protein in the lipid bilayer to those that help proteins fold into a unique three-dimensional structure? (2)d) How do cells restrict the movement of membrane proteins? Outline the different strategies and provide brief examples. (2)e) How does membrane structure allow them to have separate identities and functions on each side? (2)