MOLBIO EXAM 1 2025
QUESTIONS AND ANSWERS
100% PASS
1. What are the building blocks of DNA, RNA and proteins? What does their order in a
polymer determine? What bonds are responsible for primary information in these
polymers? What bonds are critical for shape? What are the 4 types of weak chemical
bonds/forces? - ✔✔For DNA and RNA, the building blocks are nucleotides. For
proteins, this would be amino acids. The sequence determines the structure of protein
and genetic information of DNA/RNA. Covalent bonds are responsible for primary
information. Weak bonds are important for shape along with Disulfide bridges =
covalent link between two cysteines. 4 types of weak chemical bonds/forces are
hydrogen, ionic, hydrophobic, and van der waal interactions.
2. What are the common structural features of amino acids (a.a.)? What types of R
groups are there? What are the characteristics of these R groups (ie + or - charge). -
✔✔Some common structural feature of amino acids are that they have an amino group,
carboxylic acid group, have R-groups, and a proton group. In terms of R groups, there
are neutral nonpolar, neutral polar, acidic, and basic amino acids.
Neutral nonpolar amino acids are nonpolar.
Neutral polar amino acids are polar with an OH or SH bond.
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,Acidic amino acids have a negative charge.
Basic amino acids have a positive charge.
3. What is so special about Cys, Gly and Pro. Why is Histidine's R group different from
others? What happens to a disulfide bridge in a reducing environment?
Remember...The Amino acids we looked at in class shows their ionization states at
biological (physiological) pH (~7). - ✔✔Cys - has an SH group that oxidizes to form
disulfide bridges which are a strong bond
Gly - R group is only H, not a carbon chain
Pro - R group bends around to form a ring
HIstidine R group is different from others as it is ionized at around pH 6 and at pH 7,it
could be protonated or uncharged.
Thiol gets oxidized to make a disulfide bridge. So in a reducing environment, a
disulfide bridge would break and turn into two thiols.
4. What are the characteristics of a peptide bond? If a peptide bond is rigid, how can
proteins take on different shapes? What is the difference between configuration and
conformation. - ✔✔Covalent linkage between amino acids that is rigid and has a partial
double bond character. Although peptide bond is rigid, other bonds in the backbone
can still rotate and can therefore make a 3D shape. Configuration refers to the
arrangement of parts in a polypeptide chain in an order or sequence while
conformation refers to the shape or spatial arrangements of a polypeptide chain.
5. What are the 4 levels of protein structure and their characteristics? What is the
importance of Carbonyl O and Amide H in the backbone? - ✔✔Primary structure refers
to the linear sequence of amino acids. Secondary structure refers to the interactions
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, between parts of the polypeptides IE the formation of beta sheets or alpha helices.
Tertiary structure refers to the 3D shape of a polypeptide including folds etc.
Quaternary structure refers to multiple polypeptide chains coming together. The
importance of carbonyl O and Amide H in the backbone is due to H-bonding so they
stack on top of each other to be stable.
6. What are the two most common secondary structures? What are their characteristics?
What kind of interactions are involved in tertiary structure? What is a turn (loop)? What
is a hairpin turn(loop)? - ✔✔The two most common secondary structures are Beta sheet
and alpha helices.
Beta sheets have hydrogen bonds between carbonyl O of one strand and amine H of
another to form a sheet and have 180 degrees of rotation.
Alpha helices have hydrogen bonds between carbonyl O and amine H however, they
bond 4 residues apart. Alpha helices also have their R groups protruding out of the
helix + H bond donors have the same orientation.
Regarding tertiary structure, some interactions are hydrophobic R groups cluster
internally or polar side chains hydrogen bond to each other. Also covalent bonding is
important such as Disulfide bridges forming.
A turn loop links two amino acid structures together in a very moderate turn while a
hairpin loop is a very sharp turn that links two amino acid structures together.
7. What are the 4 basic lessons we went over about the study of protein structure? When
discussing protein sequence what does I57V mean? - ✔✔1) Hydrophobic side chains
tend to cluster internally
2) Hydrophilic side chains tend to interact with the environment
3) If a hydrophilic side chain is buried internally, it is usually interacting with another
side chain to negate its hydrophilic properties
COPYRIGHT © 2025 BY GRACE AMELIA, ALL RIGHTS RESERVED 3
QUESTIONS AND ANSWERS
100% PASS
1. What are the building blocks of DNA, RNA and proteins? What does their order in a
polymer determine? What bonds are responsible for primary information in these
polymers? What bonds are critical for shape? What are the 4 types of weak chemical
bonds/forces? - ✔✔For DNA and RNA, the building blocks are nucleotides. For
proteins, this would be amino acids. The sequence determines the structure of protein
and genetic information of DNA/RNA. Covalent bonds are responsible for primary
information. Weak bonds are important for shape along with Disulfide bridges =
covalent link between two cysteines. 4 types of weak chemical bonds/forces are
hydrogen, ionic, hydrophobic, and van der waal interactions.
2. What are the common structural features of amino acids (a.a.)? What types of R
groups are there? What are the characteristics of these R groups (ie + or - charge). -
✔✔Some common structural feature of amino acids are that they have an amino group,
carboxylic acid group, have R-groups, and a proton group. In terms of R groups, there
are neutral nonpolar, neutral polar, acidic, and basic amino acids.
Neutral nonpolar amino acids are nonpolar.
Neutral polar amino acids are polar with an OH or SH bond.
COPYRIGHT © 2025 BY GRACE AMELIA, ALL RIGHTS RESERVED 1
,Acidic amino acids have a negative charge.
Basic amino acids have a positive charge.
3. What is so special about Cys, Gly and Pro. Why is Histidine's R group different from
others? What happens to a disulfide bridge in a reducing environment?
Remember...The Amino acids we looked at in class shows their ionization states at
biological (physiological) pH (~7). - ✔✔Cys - has an SH group that oxidizes to form
disulfide bridges which are a strong bond
Gly - R group is only H, not a carbon chain
Pro - R group bends around to form a ring
HIstidine R group is different from others as it is ionized at around pH 6 and at pH 7,it
could be protonated or uncharged.
Thiol gets oxidized to make a disulfide bridge. So in a reducing environment, a
disulfide bridge would break and turn into two thiols.
4. What are the characteristics of a peptide bond? If a peptide bond is rigid, how can
proteins take on different shapes? What is the difference between configuration and
conformation. - ✔✔Covalent linkage between amino acids that is rigid and has a partial
double bond character. Although peptide bond is rigid, other bonds in the backbone
can still rotate and can therefore make a 3D shape. Configuration refers to the
arrangement of parts in a polypeptide chain in an order or sequence while
conformation refers to the shape or spatial arrangements of a polypeptide chain.
5. What are the 4 levels of protein structure and their characteristics? What is the
importance of Carbonyl O and Amide H in the backbone? - ✔✔Primary structure refers
to the linear sequence of amino acids. Secondary structure refers to the interactions
COPYRIGHT © 2025 BY GRACE AMELIA, ALL RIGHTS RESERVED 2
, between parts of the polypeptides IE the formation of beta sheets or alpha helices.
Tertiary structure refers to the 3D shape of a polypeptide including folds etc.
Quaternary structure refers to multiple polypeptide chains coming together. The
importance of carbonyl O and Amide H in the backbone is due to H-bonding so they
stack on top of each other to be stable.
6. What are the two most common secondary structures? What are their characteristics?
What kind of interactions are involved in tertiary structure? What is a turn (loop)? What
is a hairpin turn(loop)? - ✔✔The two most common secondary structures are Beta sheet
and alpha helices.
Beta sheets have hydrogen bonds between carbonyl O of one strand and amine H of
another to form a sheet and have 180 degrees of rotation.
Alpha helices have hydrogen bonds between carbonyl O and amine H however, they
bond 4 residues apart. Alpha helices also have their R groups protruding out of the
helix + H bond donors have the same orientation.
Regarding tertiary structure, some interactions are hydrophobic R groups cluster
internally or polar side chains hydrogen bond to each other. Also covalent bonding is
important such as Disulfide bridges forming.
A turn loop links two amino acid structures together in a very moderate turn while a
hairpin loop is a very sharp turn that links two amino acid structures together.
7. What are the 4 basic lessons we went over about the study of protein structure? When
discussing protein sequence what does I57V mean? - ✔✔1) Hydrophobic side chains
tend to cluster internally
2) Hydrophilic side chains tend to interact with the environment
3) If a hydrophilic side chain is buried internally, it is usually interacting with another
side chain to negate its hydrophilic properties
COPYRIGHT © 2025 BY GRACE AMELIA, ALL RIGHTS RESERVED 3
