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Biol 131
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Building Blocks
You are expected to bring completed study questions to the evening study session. Answer
these study questions by referencing the relevant sections of the textbook. The written
explanations are the most important part of your answers and key to learning of concepts.
1. As part of an ambitious student research project you create a short synthetic peptide consisting of
4 amino acids. However, instead of linking the amino acids in the intended order of Trp – Gly –
Val – Ile, you accidentally synthesize peptides in the reverse order, Ile –Val – Gly – Trp. One of
your classmates says the two proteins must be identical, and bets you $20 that the peptides are
structurally and functionally equivalent. After having read this chapter, you have no hesitation in
staking your $20 that they are different. Explain why these two peptides are not identical.
2. A. Name each of the following functional groups:
O
||
–C–
___________________
– NH3
___________________
– SH
___________________
– OH
____________________
-- PO4
____________________
--COOH
___________________
-- CH3
____________________
B. Circle and label the functional groups in these molecules.
Fructose-1-P
(a monosaccharide)
Cysteine
(an amino acid)
Cytidine monophosphate
CMP (a nucleotide)
C. Explain why the Cysteine molecule shown above contains neither a hydroxyl nor a carbonyl
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Building Blocks
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3. Ionic, hydrogen and Van der Waals bonds are critical for interactions of proteins and other
molecules. These non-covalent bonds involve the AA side chains. Selecting from those listed in
the box, which type(s) of amino acids would:
A. form ionic bonds with negatively charged DNA. _________
B. form hydrogen bonds with water. __________
C. help hold together two water-soluble proteins.__________
Choices
(more than one may
be correct)
1. non-polar
2. uncharged polar
3. charged polar
D. form Van der Waals bonds between an integral
membrane protein and the lipid bilayer. _______
E. be found in the hydrophobic core of a protein ________
4. There is a lot of interest in being able to predict the structure of proteins based on their amino
acid sequence. Yet this is a daunting challenge, and requires the use of advanced super
computers. Some aspects of protein structure are more difficult than others to predict. Order
these from 1-most easy to predict to 3-most difficult to predict:
____ secondary structure, i.e., the presence of alpha helices and beta sheets
____ tertiary structure, i.e. the folding of the protein into a final 3-D form
____ quaternary structure, the specific binding between different proteins
Explain your decision:
5. Refer to the diagram to the right for this question.
A. Circle and label the different 2o structures present in this protein.
B. What is the “1o structure” of this protein?
C. Explain why the statement “this protein lacks 3o structure”
is incorrect:
D. Explain why the statement “this protein lacks 4o structure”
is correct:
E. Which levels of protein structure would be destroyed by heating to the boiling point?
Explain.
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Building Blocks
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6. The diagram to the right shows the alignment of the
amino acid chain for part of a protein.
A. Draw on the diagram hydrogen bonds where they
would be expected to occur.
B. Circle the peptide bonds along each chain.
C. How many complete amino acids are shown in the
diagram? _____
D. Label the amino and carboxyl ends of each chain.
E. Label with “--R” where the side chains would be
attached to each amino acid
F. What type of secondary structure does this diagram
represent? ____________________
7. Imagine that you have a very special microscope that allows you to photograph parts of
molecules. Using this microscope, you take a picture of samples containing different nucleic
acids, with the following results. First, indicate which possible type(s) of macromolecule you
could be looking at, and then indicate whether it contains DNA, RNA, either DNA or RNA,
neither DNA or RNA.
Sample
Image shows
Type of macromolecule
DNA/RNA/either/neither
1
Thymine
___________________
_______________
2
Alanine
___________________
_______________
3
Ribose
___________________
_______________
4
Phosphate
___________________
_______________
5
Uracil
___________________
_______________
8. The following diagrams show parts of three different types of biological macromolecules.
What types of molecule does each represent?
_________________
Biol 131
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Building Blocks
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9. Clearly describe 4 distinct cellular functions of proteins.
1.
2.
3.
4.
10. Redraw these two amino acids as they would appear after being joined by a peptide bond. Label
the amino and carboxyl ends of the peptide.
A protein comprised predominantly of these amino acids would be both ____ and ____.
A. charged
C. uncharged
E. ionic
B. polar
D. nonpolar
F. hydrophobic
11. A. Using the standard numbering system, number the carbons of these monosaccharides.
Glucose
Ribose
B. Draw phosphate groups on the carbons of the ribose on which they would occur in a nucleic
acid.
C. In a nucleotide, the nitrogenous base would be attached to carbon # ___ of the ribose. Circle
this carbon.
12. Redraw the following part of a fatty acid so that it contains a single unsaturated bond:
H H H H
| | | |
--C--C--C--C-| | | |
H H H H
13. Distinguish the structures of properties of phospholipids and triglycerides
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A. Name each of these molecules.
B. In each model, label each numbered item with the correct term selected from the list below.
C. In the spaces provided redraw each molecule in a schematic representation as shown in the
textbook figure “3.29 a.”
_________________________
schematic
Component choices
A. Phosphate
B. Non-polar head group
C. Glycerol
D. Polar head group
E. Saturated fatty acid
F. Acetic acid
G. Sugar
H. Hydrophobic region
I. Hydrophilic region
J. Non-saturated fatty acid
_________________________
schematic
D. When dispersed into water phospholipids form a colloidal suspension of very small spheres
whereas triglycerides will not mix with water at all. Explain how the molecular structures of
phospholipids and triglycerides cause these behaviors in water.
Biol 131
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Building Blocks
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