Unit2A Problem Set (1)

.pdf

School

University of British Columbia *

*We aren’t endorsed by this school

Course

200

Subject

Biology

Date

Apr 3, 2024

Type

pdf

Pages

Uploaded by ConstableWillpower8968

© 2024 – BIOL200 UBC Last updated 2024-01-04 12:11:00 AM Page 1 of 11 Unit 2, Part A, Problem Set – By Topic Based on material from Chapter 2 of the textbook: https://open.oregonstate.education/cellbiology/chapter/biological-membranes/ Topic 2.1 – The Chemical Features of Biological Membranes Learning Goals CLO refers to the course-level learning outcome, as described in the course syllabus. • List the four primary features of a biological membrane and explain why they are important for cellular function. CLO2, CLO3 • Explain how the chemical structure of a membrane (including lipids, carbohydrates and proteins) contributes to its function (as identified by the primary features listed above). CLO3 • Explain how the hydrophobic effect holds membranes together, and selectively excludes some molecules but not others. CLO2, CLO3 • Define the term ‘membrane fluidity’ in two different ways. CLO1 Topic 2.1 - Content Review Questions (i.e., Study group discussion points) 1. For the following molecules, examine the molecular structures and label the following regions (note that they may not all exist in each of the molecules: phosphatidylcholine, cholesterol, generic glycolipid, sodium dodecyl sulfate [SDS]): a. the polar region (differentiate between charged and uncharged molecules of the polar region) and the nonpolar region b. a region that would be stiff and inflexible c. a glycerol residue (Some molecules have a serine residue instead; does yours?) d. a region that could easily have C=C bonds added (How would that affect the structure of that region?) 2. For the molecules you found in Question 1, identify the lipids that would be able to form lipid bilayers on their own. Use the details of the structures that you drew to explain why or why not. 3. Define the four levels of protein folding and explain how each one is stabilized. 4. Self-assembly of macromolecules is an important concept. What do you think that means? 5. Are disulfide bridges covalent or noncovalent interactions? How do they form? Why are they considered to be uncommon in the cytosol? 6. Find images of all 20 amino acids (don’t memorize them!) online. Critically assess the structures and identify the following: a. The portion of the amino acid that is common to all of them. b. The portion that is unique to each amino acid, known as the R group or side chain.

© 2024 – BIOL200 UBC Last updated 2024-01-04 12:11:00 AM Page 2 of 11 c. 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? d. 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 neighbors. ▪ Any R groups you would consider to be “big” or “small” relative to the others.

© 2024 – BIOL200 UBC Last updated 2024-01-04 12:11:00 AM Page 3 of 11 Topic 2.1 - Practice Problems (Data analysis & problem solving. More likely to be exam-style) Problem 2.1.1 (Walkthrough Available) The experiment described here is of historical importance as it provided the first decisive evidence that the folding of proteins was dependent only on the primary structure of the protein and that it was a result of molecular self-assembly (i.e. based on chemical properties). A Nobel prize was awarded for this work way back in 1972. Background: This experiment deals with the structure and activity of ribonuclease, an enzyme that degrades RNA. It is produced in the pancreas. It is one of the first proteins for which the amino acid sequence was known. The protein's enzyme activity occurs only when the molecule is properly folded. As the molecule denatures, the enzymatic activity is lost. The molecule has 4 disulfide bonds (C- S-S -H) that hold the chain together (see picture on the right). These form between cysteine residues. If the molecule is to be completely denatured, these bonds must be broken. Disulfide bridges are broken by placing the protein in a solution of 8 M urea and beta mercaptoethanol (HS-CH 2 -CH 2 -OH, reducing agent). The urea interferes with formation of hydrogen bonds and the reducing agent provides a reducing environment, in which the disulfide bond will break, leaving 2 – SH groups (one on each cysteine). The plot on the right (top) shows how the enzymatic activity decreases as the mean number of disulfide bridges per ribonuclease molecule decreases during denaturation. Each disulfide bridge produces two SH groups: -C-S-S-C- → C-S H H S-C- (oxidized) (reduced) If the reducing agent and the urea are removed the protein will slowly oxidize in the presence of air. The S-S bonds will reform and enzyme activity is restored, as shown in the lower graph on the right (Figure 2). a) Describe how enzyme activity changes as the mean number of disulfide bridges decreases. Why do you think the enzyme activity is affected this way? b) Compare the changes in enzyme activity and reformation of S-S groups change as reoxidization progresses. What does this tell you? c) What are some of the assumptions we are making in this experiment? d) Why do you think there is a lag between the formation of S-S bonds and the restoration of enzyme activity? e) Based on the data been presented here, what did this landmark research contribute to our understanding of protein folding? (Source of data: Anfinsen et al. 1961 PNAS 47, 1309, and White 1960 J. Biol. Chemistry 235, 383)

© 2024 – BIOL200 UBC Last updated 2024-01-04 12:11:00 AM Page 4 of 11 Problem 2.1.2 The structure and chemical properties of a lipid bilayer is determined by the particular components of its lipid molecules. As a thought experiment, think about what would happen if: a) Phospholipids had only one hydrocarbon tail instead of two? b) The hydrocarbon tails were much shorter than normal, say, about 10 carbon atoms or less? c) All of the hydrocarbon chains were saturated? d) Would you expect the permeability of a synthetic membrane, made entirely of phospholipids, to be greater or less than that of a ‘real’ membrane? Why? e) Would you expect a single-celled, freshwater organism have a membrane that is more or less permeable than a single-celled marine organism? Why? Problem 2.1.3 Here are partial amino acid sequences of normal human hemoglobin and three variants (mutants) that occur normally in the human population. Some of these hemoglobin molecules lead to defective function of the molecules while others function quite normally. a) Which version is most likely to result in a phenotypically "silent" mutation? Why? b) Which version is likely to result in the largest disruption of the three-dimensional structure of the protein? Why? Problem 2.1.4 Explain why it would be incorrect to say the following: a) Lipids in a lipid bilayer are immobile. b) Lipids in a lipid bilayer rapidly flip from one leaflet to the other. c) When a protein is made of more than one polypeptide, disulfide bridges must be used to hold the two subunits together. d) Oxygen and water molecules cannot pass through a lipid bilayer unless there are proteins present. e) Lipid bilayers are assembled with the help of chaperone proteins. f) A lipid bilayer and a biological membrane are synonyms of each other. They define exactly the same thing.

Your preview ends here

Eager to read complete document? Join bartleby learn and gain access to the full version