Protein structure— formative assessment AP Biology 10/7/2013

Level 2.0

1. What is the name for the variable region of the 20 amino acids? 1.Carboxyl group 2.Amino group 3.R group 4.Alpha Carbon

2. What functional group must be present in the R group of an acidic (-) amino acid? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.Carbonyl group 5.Sulfahydryl group

3. What functional group must be present in the R group of a basic (+) amino acid? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.Carbonyl group 5.Sulfahydryl group

4. What functional group is most often present in a neutral, yet hydrophilic, amino acid’s R group? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.phosphate group 5.sulfahydryl

5. What functional group in cysteine and methionine allows them to form strong covalent bonds that stabilize a protein’s tertiary structure? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.Carbonyl group 5.Sulfahydryl group

6. Which arrow points to a peptide bond? 1.a 2.b 3.c 4.d a ab c d

Level 3.0

7. How do alpha helices and Beta pleated sheets compare? 1.They are both forms of protein secondary structure 2.They are both formed due to formation of H bonds between N-H & C=O groups along the backbone of polypeptide chain 3.The beta sheets are more rigid & strong because they form more abundant H bonds 4.All of the above

8. R group interactions control which levels of protein folding? 1.Primary structure & secondary structure 2.Secondary structure only 3.Tertiary & quartenary structure 4.Tertiary structure only 5.Quartenary structure only

9. Which amino acids tend to cluster in the center of an aqueous protein, but to be located on the outer edges of proteins located within a cell membrane’s lipid bilayer? 1.Acidic amino acids 2.Basic amino acids 3.Disulfide bridge forming cysteines & methionines 4.Polar, hydrophilic amino acids 5.Nonpolar, hydrophobic amino acids

10 Primary protein structure A.Is directly defined by the genetic code B.Is the linear order of amino acids C.Includes peptide bonds of the backbone D.All of the above

11. Secondary structure is due to: A.Peptide bonding B.R group acidic & basic interaction C.H bonding between carbonyl & amino groups of backbone D.H bonding between carboxyl & amino groups in R groups of different amino acids

12. Which interactions are most important in making denatured proteins clump together? A.Acid/base R group interaction B.Hydrophobic R group interactions C.Hydrophilic R group interactions D.Disulfide bridges

13. Write the order of strength of these interactions in determining tertiary structure? A.Vanderwaals forces of hydrophobic R group interactions B.Hydrogen bonding of hydrophilic, yet neutral R group interactions C.Acidic & Basic R group interactions D.Disulfide bridges of methionine to methionine or cysteine to cysteine

14. Give an example of a quarternary structure. Enter Answer Text

If your answers were correct for 8 or 9 questions, then you should work independently on Stanford notes for Chapter 6. This power point will be online for your use in studying. If you answered 7 or fewer questions correctly, you should review the next explanation slides.

1. What is the name for the variable region of the 20 amino acids? 1.Carboxyl group 2.Amino group 3.R group 4.Alpha Carbon

Every amino acid contains a central (α) C, surrounded by a H, an R group (variable group), an amino group, and a carboxyl group. The amino group acts as a base, accepting a protons, whereas the carboxyl group acts as an acid, donating a proton.

2. What functional group must be present in the R group of an acidic (-) amino acid? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.Carbonyl group 5.Sulfahydryl group

About 1 x Moles water /L dissociates to produce H + ions and OH - ions. The ratio of the two ions is 1.0, and the pH is 7—neutral. When substances known as acids are dissolved in water, then they dissociate to produce H + ions, making the H + :OH - ratio higher than 1.0. Acids are proton donors when dissolved in aqueous solution. Carboxyl groups behave as acids because they dissociate to release H + ions. The amino acids aspartic acid & glutamic acids have a carboxyl group in their group, so they are acidic amino acids.

3. What functional group must be present in the R group of a basic (+) amino acid? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.Carbonyl group 5.Sulfahydryl group

Bases either release OH - OR accept H + ions when dissolved in aqueous solution. In both cases, bases reduce the H + : OH - ratio to less than 1.0 The amino group in an amino acid’s R group acts as a base, accepting a proton. The amino acids arginine and lysine act as bases.

4. What functional group is most often present in a neutral, yet hydrophilic, amino acid’s R group? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.Carbonyl group 5.sulfahydryl

5. What functional group in cysteine and methionine allows them to form strong covalent bonds that stabilize a protein’s tertiary structure? 1.Carboxyl group 2.Amino group 3.Hydroxyl group 4.Carbonyl group 5.Sulfahydryl group

6. Which arrow points to a peptide bond? 1.a 2.b 3.c 4.d a ab c d

Level 3.0

7. How do alpha helices and Beta pleated sheets compare? 1.They are both forms of protein secondary structure 2.They are both formed due to formation of H bonds between N-H & C=O groups along the backbone of polypeptide chain 3.The beta sheets are more rigid & strong because they form more abundant H bonds 4.All of the above

Protein structure

8. R group interactions control which levels of protein folding? 1.Primary structure & secondary structure 2.Secondary structure only 3.Tertiary & quartenary structure 4.Tertiary structure only 5.Quartenary structure only

R group interactions control tertiary & Quarternary structure

9. Which amino acids tend to cluster in the center of an aqueous protein, but to be located on the outer edges of proteins located within a cell membrane’s lipid bilayer? 1.Acidic amino acids 2.Basic amino acids 3.Disulfide bridge forming cysteines & methionines 4.Polar, hydrophilic amino acids 5.Nonpolar, hydrophobic amino acids