BIOL 355 - 2025 Summer Name: Name is written on every page.
Exam 1 Date:
Write your name on each page; points will be deducted for omitted names. Write concise, precise (not
run-on) sentences or lists, as appropriate. Do not exceed the sentence limit or space provided. Read all
instructions carefully.
1. For this question, you may write full names or conventional abbreviations. (Total: 16 points)
Amino Acid(s)
cysteine (Cys, C) (4 points)
A. An antibody is composed of several polypeptides. The separate
polypeptides are covalently attached to one another. Which amino
acid(s) mediate these attachments?
B. Histones are an important component of chromatin. Histones arginine (Arg, R) and lysine
(Lys, K) (4 points) *
interact with the phosphates of DNA. Which amino acid(s) mediate
these interactions?
C. Protein phosphorylation can serve as a binding site or a switch serine (Ser, S), threonine (Thr, T),
during cell signaling. Which amino acid(s) can be phosphorylated on and tyrosine (Tyr, Y) (4 points) *
their side chains?
D. Signal sequences play critical roles in the localization of two nonpolar amino acids (see
membrane proteins and secreted proteins. Name two amino acids Panel 3-1 in Molecular Biology of
that likely could be found in these signal sequences. the Cell ) (4 points)
* Note: Histidine (His, H) (basic; can be phosphorylated) is not required for full credit.
2. Your study partner, who is interested in teaching, reads Vision and Change in Undergraduate Biology
Education (AAAS & NSF, 2009) and calls your attention to the following statement: “In our discussions, we
came to a consensus that five organizing themes describe lines of inquiry in modern biology and, thereby, help
define core concepts for the discipline. … After much discussion and debate, Vision and Change participants
agreed that all undergraduates should develop a basic understanding of the following core concepts.” (Total:
12 points)
A. With regard to the core concept of evolution , your study partner challenges you to identify which
compartments of a cell are “outside” of the cell and to explain, evolutionarily, why. Consider cytosol,
endomembrane system, mitochondria/chloroplasts, and nucleus. Limit: 2 sentences.
Lumens of endomembrane system and intermembrane spaces of mitochondria/chloroplasts are
“outside” because they evolved from invaginations of plasma membranes (4 points).
B. With regard to the core concept of structure and function , your study partner challenges you to
explain how the structure of a phospholipid results in transverse diffusion that is slower than
lateral diffusion.
Limit: 2 sentences.
Hydrophilic heads do not readily move through regions of hydrophobic tails (4 points).
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, BIOL 355 - 2025 Summer Name: Name is written on every page.
Exam 1 Date:
C. With regard to the core concept of information flow, exchange, and storage , your study partner
challenges you to explain where the information that specifies the location of a plasma membrane
protein resides. Limit: 2 sentences.
Because the signal(s) are part of the plasma membrane protein, the information resides in the
genetic material (i.e., DNA, mRNA) and the protein itself (4 points).
3. The evolutionary origin of the peroxisome, as well as its relationship to the endomembrane system, is
still controversial. (Total: 16 points)
Propose alternative hypotheses for the evolutionary
Identify one aspect of peroxisome biogenesis, as
origin of the peroxisome. Limit: 1 sentence. illustrated above, that supports your hypothesis.
Limit: 1 sentence.
Hypothesis A: The peroxisome evolved from the Vesicular transport from the ER contributes to
endomembrane system (or ER) (4 points). peroxisome biogenesis (4 points).
Hypothesis B: Several answers are possible. For Uptake from the cytosol contributes to
example, the peroxisome evolved from an peroxisome biogenesis (4 points). Alternatively,
endosymbiotic event (4 points). the peroxisome undergoes fission.
4. You are discussing BQMOC with a colleague who has not yet taken BIOL 355. Explain to your
colleague the relationships between the following BQMOC components. For example, how are they
interconnected? How are they different? (Total: 8 points)
A. Background and C onclusion. Limit: 2 sentences.
Background is known from previous research, whereas c onclusions arise from the
current research (4 points). Or, one figure’s c onclusions can become a subsequent
figure’s b ackground. Alternatively, b ackground sets up q uestions, whereas
c onclusions answer q uestions.
Page 2
Exam 1 Date:
Write your name on each page; points will be deducted for omitted names. Write concise, precise (not
run-on) sentences or lists, as appropriate. Do not exceed the sentence limit or space provided. Read all
instructions carefully.
1. For this question, you may write full names or conventional abbreviations. (Total: 16 points)
Amino Acid(s)
cysteine (Cys, C) (4 points)
A. An antibody is composed of several polypeptides. The separate
polypeptides are covalently attached to one another. Which amino
acid(s) mediate these attachments?
B. Histones are an important component of chromatin. Histones arginine (Arg, R) and lysine
(Lys, K) (4 points) *
interact with the phosphates of DNA. Which amino acid(s) mediate
these interactions?
C. Protein phosphorylation can serve as a binding site or a switch serine (Ser, S), threonine (Thr, T),
during cell signaling. Which amino acid(s) can be phosphorylated on and tyrosine (Tyr, Y) (4 points) *
their side chains?
D. Signal sequences play critical roles in the localization of two nonpolar amino acids (see
membrane proteins and secreted proteins. Name two amino acids Panel 3-1 in Molecular Biology of
that likely could be found in these signal sequences. the Cell ) (4 points)
* Note: Histidine (His, H) (basic; can be phosphorylated) is not required for full credit.
2. Your study partner, who is interested in teaching, reads Vision and Change in Undergraduate Biology
Education (AAAS & NSF, 2009) and calls your attention to the following statement: “In our discussions, we
came to a consensus that five organizing themes describe lines of inquiry in modern biology and, thereby, help
define core concepts for the discipline. … After much discussion and debate, Vision and Change participants
agreed that all undergraduates should develop a basic understanding of the following core concepts.” (Total:
12 points)
A. With regard to the core concept of evolution , your study partner challenges you to identify which
compartments of a cell are “outside” of the cell and to explain, evolutionarily, why. Consider cytosol,
endomembrane system, mitochondria/chloroplasts, and nucleus. Limit: 2 sentences.
Lumens of endomembrane system and intermembrane spaces of mitochondria/chloroplasts are
“outside” because they evolved from invaginations of plasma membranes (4 points).
B. With regard to the core concept of structure and function , your study partner challenges you to
explain how the structure of a phospholipid results in transverse diffusion that is slower than
lateral diffusion.
Limit: 2 sentences.
Hydrophilic heads do not readily move through regions of hydrophobic tails (4 points).
Page 1
, BIOL 355 - 2025 Summer Name: Name is written on every page.
Exam 1 Date:
C. With regard to the core concept of information flow, exchange, and storage , your study partner
challenges you to explain where the information that specifies the location of a plasma membrane
protein resides. Limit: 2 sentences.
Because the signal(s) are part of the plasma membrane protein, the information resides in the
genetic material (i.e., DNA, mRNA) and the protein itself (4 points).
3. The evolutionary origin of the peroxisome, as well as its relationship to the endomembrane system, is
still controversial. (Total: 16 points)
Propose alternative hypotheses for the evolutionary
Identify one aspect of peroxisome biogenesis, as
origin of the peroxisome. Limit: 1 sentence. illustrated above, that supports your hypothesis.
Limit: 1 sentence.
Hypothesis A: The peroxisome evolved from the Vesicular transport from the ER contributes to
endomembrane system (or ER) (4 points). peroxisome biogenesis (4 points).
Hypothesis B: Several answers are possible. For Uptake from the cytosol contributes to
example, the peroxisome evolved from an peroxisome biogenesis (4 points). Alternatively,
endosymbiotic event (4 points). the peroxisome undergoes fission.
4. You are discussing BQMOC with a colleague who has not yet taken BIOL 355. Explain to your
colleague the relationships between the following BQMOC components. For example, how are they
interconnected? How are they different? (Total: 8 points)
A. Background and C onclusion. Limit: 2 sentences.
Background is known from previous research, whereas c onclusions arise from the
current research (4 points). Or, one figure’s c onclusions can become a subsequent
figure’s b ackground. Alternatively, b ackground sets up q uestions, whereas
c onclusions answer q uestions.
Page 2
