USABO FINAL EXAM QUESTIONS WITH SOLUTIONS 2025 GRADED
A+
✔✔Tertiary Structure - ✔✔In biochemistry and molecular biology, this structure of a
protein or any other macromolecule is its three-dimensional structure, as defined by the
atomic coordinates.[6] Proteins and nucleic acids are capable of diverse functions
ranging from molecular recognition to catalysis. Such functions require a precise three-
dimensional tertiary structure. While such structures are diverse and seemingly
complex, they are composed of recurring, easily recognizable tertiary structure motifs
that serve as molecular building blocks. Tertiary structure is considered to be largely
determined by the biomolecule's primary structure, or the sequence of amino acids or
nucleotides of which it is composed. Efforts to predict tertiary structure from the primary
structure are known generally as structure prediction.
✔✔Primary Structure - ✔✔This is the name given to the sequence of amino acid
monomer units, or residues of which a compound is composed.
✔✔Alpha carbon - ✔✔The carbon bonded to the carboxyl group in an amino acid.
✔✔R Group - ✔✔This is the group which varies in proteins and can be any of twenty
amino acids, the polarity of this Group dictates how a protein will behave in certain pH
conditions. This explains why enzymes require a certain pH to function.
✔✔Peptide Bond - ✔✔This bond occurs when the amino group from one protein joins
with the carboxyl group of another, forming a dipeptide.
✔✔Dipeptide - ✔✔A protein formed by two amino acids linked by a peptide bond,
✔✔Amino Terminus - ✔✔The name by which the -NH₂ free end of a peptide is known.
✔✔Carboxyl Terminus - ✔✔The name by which the -COOH (carboxyl) free end of a
peptide is known.
✔✔Peptide - ✔✔Small chains of amino acids.
✔✔Mr - ✔✔Shorthand for molecular mass.
✔✔Hydrophobic residues/amino acid - ✔✔Amino acids which are non polar and are
repelled by water example are Alanine, Valine, Leucine, Isoleucine, Proline, Methionine,
Phenylalanine, Tryptophan and Cystine. Hydrophbicity is also affected by pH levels in
some cases.
✔✔Hydrophillic residues/amino acid - ✔✔Amino acids which are polar and are attracted
to water examples are Glutamine, Serine,Theronine, Histodine, Lysine. Hydrophbicity is
also affected by pH levels in some cases.
,✔✔Polar - ✔✔Pertaining to a compound exhibiting polarity or dipole moment, that is a
compound bearing a partial positive charge on one side and a partial negative charge
on the other.
✔✔Non Polar - ✔✔Molecule which has no separation of charge, so no positive or
negative poles are formed.
✔✔α Helix - ✔✔A common motif in the secondary structure of proteins, the alpha helix
(α-helix) is a right-handed coiled or spiral conformation, in which every backbone N-H
group donates a hydrogen bond to the backbone C=O group of the amino acid four
residues earlier (i+4 \rightarrow i hydrogen bonding). This secondary structure is also
sometimes called a classic Pauling-Corey-Branson alpha helix . Among types of local
structure in proteins, the α-helix is the most regular and the most predictable from
sequence, as well as the most prevalent.
✔✔β sheet - ✔✔The β sheet (also β-pleated sheet) is the second form of regular
secondary structure in proteins, only somewhat less common than alpha helix. Beta
sheets consist of beta strands connected laterally by at least two or three backbone
hydrogen bonds, forming a generally twisted, pleated sheet. A beta strand (also β
strand) is a stretch of polypeptide chain typically 3 to 10 amino acids long with
backbone in an almost fully extended conformation. The higher-level association of β
sheets has been implicated in formation of the protein aggregates and fibrils observed
in many human diseases, notably the amyloidoses such as Alzheimer's disease.
✔✔Zymogens - ✔✔A zymogen (or proenzyme) is an inactive enzyme precursor. A
zymogen requires a biochemical change (such as a hydrolysis reaction revealing the
active site, or changing the configuration to reveal the active site) for it to become an
active enzyme. The biochemical change usually occurs in a lysosome where a specific
part of the precursor enzyme is cleaved in order to activate it. The amino acid chain that
is released upon activation is called the activation peptide.
The pancreas secretes zymogens partly to prevent the enzymes from digesting proteins
in the cells in which they are synthesised. Fungi also secrete digestive enzymes into the
environment as zymogens. The external environment has a different pH than inside the
fungal cell and this changes the zymogen's structure into an active enzyme.
✔✔Proteolyisis - ✔✔This process is the directed degradation (digestion) of proteins
which fail to fold correctly by cellular enzymes called proteases or by intramolecular
digestion.
✔✔Proteasomes - ✔✔Proteasomes are very large protein complexes inside all
eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the
nucleus and the cytoplasm.The main function of the proteasome is to degrade
unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide
bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are
,part of a major mechanism by which cells regulate the concentration of particular
proteins and degrade misfolded proteins. The degradation process yields peptides of
about seven to eight amino acids long, which can then be further degraded into amino
acids and used in synthesizing new proteins. Proteins to be destroyed are labelled by
ubiquitin.
✔✔Ubiquitin - ✔✔A small regulatory protein that has been found in almost all tissues
(ubiquitously) of eukaryotic organisms. Among other functions, it directs protein
recycling.It can be attached to proteins and label them for destruction. This protein tag
directs proteins to the proteasome, which is a large protein complex in the cell that
degrades and recycles unneeded proteins. This discovery won the Nobel Prize for
chemistry in 2004.
The tags can also direct proteins to other locations in the cell, where they control other
protein and cell mechanisms.
✔✔Post-translation modification - ✔✔This is the chemical modification of a protein after
its translation. It is one of the later steps in protein biosynthesis, and thus gene
expression, for many proteins.A protein (also called a polypeptide) is a chain of amino
acids. During protein synthesis, 20 different amino acids can be incorporated to become
a protein. After translation, the posttranslational modification of amino acids extends the
range of functions of the protein by attaching it to other biochemical functional groups
(such as acetate, phosphate, various lipids and carbohydrates), changing the chemical
nature of an amino acid (e.g. citrullination), or making structural changes (e.g. formation
of disulfide bridges).Also, enzymes may remove amino acids from the amino end of the
protein, or cut the peptide chain in the middle. For instance, the peptide hormone insulin
is cut twice after disulfide bonds are formed, and a propeptide is removed from the
middle of the chain; the resulting protein consists of two polypeptide chains connected
by disulfide bonds. Also, most nascent polypeptides start with the amino acid
methionine because the "start" codon on mRNA also codes for this amino acid. This
amino acid is usually taken off during post-translational modification.Other
modifications, like phosphorylation, are part of common mechanisms for controlling the
behavior of a protein, for instance activating or inactivating an enzyme.
✔✔Enzyme Substrate Complex - ✔✔A non-covalent complex composed of a substrate
bound to the active site of the enzyme
✔✔Substrate - ✔✔In biochemistry, a substrate is a molecule upon which an enzyme
acts. Enzymes catalyze chemical reactions involving the substrate(s). In the case of a
single substrate, the substrate binds with the enzyme active site, and an enzyme-
substrate complex is formed. The substrate is transformed into one or more products,
which are then released from the active site. The active site is now free to accept
another substrate molecule. In the case of more than one substrate, these may bind in a
particular order to the active site, before reacting together to produce products.
, ✔✔Substrate specificity - ✔✔A characteristic feature of enzyme activity in relation to the
kind of substrate on which the enzyme or catalytic molecule reacts. An ezyme can only
react upon the substrate with which it locks.
✔✔Enzyme Assay - ✔✔A technique used to measure the rate of activity of an enzyme
by measuring the products expected of the enzyme activity, for example CO₂.
✔✔Km - ✔✔The point on a rectangular hyperbola which is half the value of the Vmax. It
indicates the affinity of an enzyme and substrate a high value means low affinity and a
low value means high affinity (the enzyme substrate locks more securely and takes
longer to seperate and release products).
✔✔Vmax - ✔✔The point on a hyperbolic plot/during an enzyme assay at which the
maximum rate of substrate to product conversion is reached and the line begins to level
out. This is often used to indicate the maximum rate of enzyme activity, however it is
only approximate as the plot line never completely levels out.
✔✔Michaelis-Menton equation - ✔✔This equation can be used if a range of [S] values
is known, to plot a line.
E + S ↔ ES → E + P
✔✔Hofstee-Eadie plot - ✔✔A plot used to obtain a more accurate indication of Km and
Vmax. Simplified - v/[S] so the figures used to plot the original hyperbolic rectangle are
used dviding the enzyme byt hte substrate. These new figures are then plotted on along
the horizontal axis and a best fit line drawn along them. The point at which the line
crosses the vertical axis is the Vmax, the point at which it crosses the horizontal axis is
the Km.
✔✔pH Optima - ✔✔The optimum pH in which an enzyme is most active, this is normally
related to the normal environment of the enzyme, for example Pepsin has a pH optima
of around 2, ideal for the acidic environment of the vertebrate stomach.
✔✔Cofactors - ✔✔Other conditions required by enzymes in order for them to perform
their roles. For example metal ions (Mg²⁺ + K⁺) or coenzymes such as NDP, ATP or
ADP. They cannot be made in the body of mammals and must be derived from vitamins
in the diet.
✔✔Enzyme Inhibition - ✔✔An important control mechanism in metabolism, this is also
the route of effect used by many drugs and also of many toxins.
✔✔Irreversible Inhibitors - ✔✔Usually not of biological origins, these act by forming
strong covalent bonds with the enzyme, poisoning them. The bond is so strong it is
irreversible and example of this would be heavy metal toxicity.
A+
✔✔Tertiary Structure - ✔✔In biochemistry and molecular biology, this structure of a
protein or any other macromolecule is its three-dimensional structure, as defined by the
atomic coordinates.[6] Proteins and nucleic acids are capable of diverse functions
ranging from molecular recognition to catalysis. Such functions require a precise three-
dimensional tertiary structure. While such structures are diverse and seemingly
complex, they are composed of recurring, easily recognizable tertiary structure motifs
that serve as molecular building blocks. Tertiary structure is considered to be largely
determined by the biomolecule's primary structure, or the sequence of amino acids or
nucleotides of which it is composed. Efforts to predict tertiary structure from the primary
structure are known generally as structure prediction.
✔✔Primary Structure - ✔✔This is the name given to the sequence of amino acid
monomer units, or residues of which a compound is composed.
✔✔Alpha carbon - ✔✔The carbon bonded to the carboxyl group in an amino acid.
✔✔R Group - ✔✔This is the group which varies in proteins and can be any of twenty
amino acids, the polarity of this Group dictates how a protein will behave in certain pH
conditions. This explains why enzymes require a certain pH to function.
✔✔Peptide Bond - ✔✔This bond occurs when the amino group from one protein joins
with the carboxyl group of another, forming a dipeptide.
✔✔Dipeptide - ✔✔A protein formed by two amino acids linked by a peptide bond,
✔✔Amino Terminus - ✔✔The name by which the -NH₂ free end of a peptide is known.
✔✔Carboxyl Terminus - ✔✔The name by which the -COOH (carboxyl) free end of a
peptide is known.
✔✔Peptide - ✔✔Small chains of amino acids.
✔✔Mr - ✔✔Shorthand for molecular mass.
✔✔Hydrophobic residues/amino acid - ✔✔Amino acids which are non polar and are
repelled by water example are Alanine, Valine, Leucine, Isoleucine, Proline, Methionine,
Phenylalanine, Tryptophan and Cystine. Hydrophbicity is also affected by pH levels in
some cases.
✔✔Hydrophillic residues/amino acid - ✔✔Amino acids which are polar and are attracted
to water examples are Glutamine, Serine,Theronine, Histodine, Lysine. Hydrophbicity is
also affected by pH levels in some cases.
,✔✔Polar - ✔✔Pertaining to a compound exhibiting polarity or dipole moment, that is a
compound bearing a partial positive charge on one side and a partial negative charge
on the other.
✔✔Non Polar - ✔✔Molecule which has no separation of charge, so no positive or
negative poles are formed.
✔✔α Helix - ✔✔A common motif in the secondary structure of proteins, the alpha helix
(α-helix) is a right-handed coiled or spiral conformation, in which every backbone N-H
group donates a hydrogen bond to the backbone C=O group of the amino acid four
residues earlier (i+4 \rightarrow i hydrogen bonding). This secondary structure is also
sometimes called a classic Pauling-Corey-Branson alpha helix . Among types of local
structure in proteins, the α-helix is the most regular and the most predictable from
sequence, as well as the most prevalent.
✔✔β sheet - ✔✔The β sheet (also β-pleated sheet) is the second form of regular
secondary structure in proteins, only somewhat less common than alpha helix. Beta
sheets consist of beta strands connected laterally by at least two or three backbone
hydrogen bonds, forming a generally twisted, pleated sheet. A beta strand (also β
strand) is a stretch of polypeptide chain typically 3 to 10 amino acids long with
backbone in an almost fully extended conformation. The higher-level association of β
sheets has been implicated in formation of the protein aggregates and fibrils observed
in many human diseases, notably the amyloidoses such as Alzheimer's disease.
✔✔Zymogens - ✔✔A zymogen (or proenzyme) is an inactive enzyme precursor. A
zymogen requires a biochemical change (such as a hydrolysis reaction revealing the
active site, or changing the configuration to reveal the active site) for it to become an
active enzyme. The biochemical change usually occurs in a lysosome where a specific
part of the precursor enzyme is cleaved in order to activate it. The amino acid chain that
is released upon activation is called the activation peptide.
The pancreas secretes zymogens partly to prevent the enzymes from digesting proteins
in the cells in which they are synthesised. Fungi also secrete digestive enzymes into the
environment as zymogens. The external environment has a different pH than inside the
fungal cell and this changes the zymogen's structure into an active enzyme.
✔✔Proteolyisis - ✔✔This process is the directed degradation (digestion) of proteins
which fail to fold correctly by cellular enzymes called proteases or by intramolecular
digestion.
✔✔Proteasomes - ✔✔Proteasomes are very large protein complexes inside all
eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the
nucleus and the cytoplasm.The main function of the proteasome is to degrade
unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide
bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are
,part of a major mechanism by which cells regulate the concentration of particular
proteins and degrade misfolded proteins. The degradation process yields peptides of
about seven to eight amino acids long, which can then be further degraded into amino
acids and used in synthesizing new proteins. Proteins to be destroyed are labelled by
ubiquitin.
✔✔Ubiquitin - ✔✔A small regulatory protein that has been found in almost all tissues
(ubiquitously) of eukaryotic organisms. Among other functions, it directs protein
recycling.It can be attached to proteins and label them for destruction. This protein tag
directs proteins to the proteasome, which is a large protein complex in the cell that
degrades and recycles unneeded proteins. This discovery won the Nobel Prize for
chemistry in 2004.
The tags can also direct proteins to other locations in the cell, where they control other
protein and cell mechanisms.
✔✔Post-translation modification - ✔✔This is the chemical modification of a protein after
its translation. It is one of the later steps in protein biosynthesis, and thus gene
expression, for many proteins.A protein (also called a polypeptide) is a chain of amino
acids. During protein synthesis, 20 different amino acids can be incorporated to become
a protein. After translation, the posttranslational modification of amino acids extends the
range of functions of the protein by attaching it to other biochemical functional groups
(such as acetate, phosphate, various lipids and carbohydrates), changing the chemical
nature of an amino acid (e.g. citrullination), or making structural changes (e.g. formation
of disulfide bridges).Also, enzymes may remove amino acids from the amino end of the
protein, or cut the peptide chain in the middle. For instance, the peptide hormone insulin
is cut twice after disulfide bonds are formed, and a propeptide is removed from the
middle of the chain; the resulting protein consists of two polypeptide chains connected
by disulfide bonds. Also, most nascent polypeptides start with the amino acid
methionine because the "start" codon on mRNA also codes for this amino acid. This
amino acid is usually taken off during post-translational modification.Other
modifications, like phosphorylation, are part of common mechanisms for controlling the
behavior of a protein, for instance activating or inactivating an enzyme.
✔✔Enzyme Substrate Complex - ✔✔A non-covalent complex composed of a substrate
bound to the active site of the enzyme
✔✔Substrate - ✔✔In biochemistry, a substrate is a molecule upon which an enzyme
acts. Enzymes catalyze chemical reactions involving the substrate(s). In the case of a
single substrate, the substrate binds with the enzyme active site, and an enzyme-
substrate complex is formed. The substrate is transformed into one or more products,
which are then released from the active site. The active site is now free to accept
another substrate molecule. In the case of more than one substrate, these may bind in a
particular order to the active site, before reacting together to produce products.
, ✔✔Substrate specificity - ✔✔A characteristic feature of enzyme activity in relation to the
kind of substrate on which the enzyme or catalytic molecule reacts. An ezyme can only
react upon the substrate with which it locks.
✔✔Enzyme Assay - ✔✔A technique used to measure the rate of activity of an enzyme
by measuring the products expected of the enzyme activity, for example CO₂.
✔✔Km - ✔✔The point on a rectangular hyperbola which is half the value of the Vmax. It
indicates the affinity of an enzyme and substrate a high value means low affinity and a
low value means high affinity (the enzyme substrate locks more securely and takes
longer to seperate and release products).
✔✔Vmax - ✔✔The point on a hyperbolic plot/during an enzyme assay at which the
maximum rate of substrate to product conversion is reached and the line begins to level
out. This is often used to indicate the maximum rate of enzyme activity, however it is
only approximate as the plot line never completely levels out.
✔✔Michaelis-Menton equation - ✔✔This equation can be used if a range of [S] values
is known, to plot a line.
E + S ↔ ES → E + P
✔✔Hofstee-Eadie plot - ✔✔A plot used to obtain a more accurate indication of Km and
Vmax. Simplified - v/[S] so the figures used to plot the original hyperbolic rectangle are
used dviding the enzyme byt hte substrate. These new figures are then plotted on along
the horizontal axis and a best fit line drawn along them. The point at which the line
crosses the vertical axis is the Vmax, the point at which it crosses the horizontal axis is
the Km.
✔✔pH Optima - ✔✔The optimum pH in which an enzyme is most active, this is normally
related to the normal environment of the enzyme, for example Pepsin has a pH optima
of around 2, ideal for the acidic environment of the vertebrate stomach.
✔✔Cofactors - ✔✔Other conditions required by enzymes in order for them to perform
their roles. For example metal ions (Mg²⁺ + K⁺) or coenzymes such as NDP, ATP or
ADP. They cannot be made in the body of mammals and must be derived from vitamins
in the diet.
✔✔Enzyme Inhibition - ✔✔An important control mechanism in metabolism, this is also
the route of effect used by many drugs and also of many toxins.
✔✔Irreversible Inhibitors - ✔✔Usually not of biological origins, these act by forming
strong covalent bonds with the enzyme, poisoning them. The bond is so strong it is
irreversible and example of this would be heavy metal toxicity.
