CHEM210 / CHEM 210 Module 3: (Latest Update
2026 / 2027) Organic Chemistry | Questions &
Answers | Grade A | 100% Correct – Portage
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Q: True or False: the amino acids serine and methionine both contain sulfur atoms.
Answer
false
Q: True or False: The following secondary structure shown below is an example of a
beta-turn.
Answer
False
Q: True or False: The side chain of proline is bonded to the backbone nitrogen atom.
Answer
True
Q: True or False: The name of the molecule that binds to an enzyme is called the
apoenzyme.
Answer
False
Q: True or False: An inhibitor that binds at the active site is an uncompetitive
inhibitor.
Answer
False
Q: Which amino acids differ by only one atom?
Ser and Thr
Leu and Ile
Ala and Ser
Asp and Asn
Ser and Cys
Answer
Ser and Cys
Q: The formation of a peptide bond between two amino acids is an example of a(n)
________ reaction.
Answer
Condensation
Q: The peptide Ala-Glu-Gly-Ala-Leu-Arg has __________.
A disulfide bond
Five peptide bonds
Four peptide bonds
A proline residue
No C-Terminal
Answer
Five peptide bonds
Q: Formally, when there are 100 or more amino acids covalently linked together that
is called a __________.
Answer
Protein
Q: What is used by biochemists to indicate the mass of a protein?
Answer
kDa or Da
Q: All of the 20 standard amino acids contain an R-group that is attached to the:
Answer
Alpha Carbon
Q: Which of the following correctly matches the amino acid with its one letter
abbreviation?
Glutamic acid, E
Isoleucine, S
Lysine, L
Phenylalanine, P
Arginine, A
Answer
Glutamic Acid, E or Aspartic Acid, D
Q: The order of amino acids in a protein is written_________.
Answer
N to C-Terminus
Q: Roughly how many amino acids are there in one turn of an alpha helix?
Answer
3.6
Q: In an alpha helix, the R groups on the amino acid residues:
Answer
are found on the outside of the helix spiral
Q: Motifs are classified primarily by their:
Answer
Content and arrangement of the secondary structure
Q: A single folded polypeptide has a globular shape, which describes its
______________ structure.
Answer
Tertiary
Q: How many classes of enzymes are recognized by the IUBMB?
Answer
6
Q: An enzyme requires Cr+3 for catalysis. When the enzyme contains the Cr+3 its
called a(n) ________________.
Answer
Holoenzyme
Q: When a substrate has just started its conversion to a new molecule, it is said to be
in the ______________.
Answer
Transition state
Q: Which of the following would change the rate of an enzyme-catalyzed reaction?
Amino acids, concentration, temp
ph, concentration, temp
ph, polarity, concentration
polarity, concentration, temp
ph, polarity, temp
Answer
ph, concentration, temp
Q: The concept of induced fit refers to the fact that:
Answer
Substrate binding induces a conformation change in the enzyme
Q: The ES stands for:
Answer
Enzyme substrate
Q: any molecule or ion that is necessary for an enzymes function is called a
___________.
Answer
cofactor
Q: Is the following protein globular or fibrous? Explain. Also identify the types of
secondary structures present in the following protein.
Answer
Its a globular protein due to its ball-like shape. Fibrous proteins are long and extended.
The types of secondary structures present are alpha helices, beta sheets and turns.
There are collections of protein structure that fit between true secondary and true
tertiary structure. what is the name of the collections of protein structure? explain the
type of structure.
Answer
Motifs occupy a position between secondary and tertiary. motifs are particularly stable
arrangements of secondary structure, including the connections between them. motifs
are found in a variety of proteins from across all organisms.
What is the lowest level of protein structure? How do scientists communicate
information about this level?
Answer
the primary level is the order of amino acids covalently bonded together including
disulfide bonds, in a polypeptide chain. the primary sequence is written for proteins
from n to c terminal using the one letter or three letter abbreviations.
What is the spot on an enzyme where reactions take place? Explain the characteristics of
this spot.
Answer
the spot of the enzyme where catalysis takes place. this area is often small when
compared to the overall size of the protein. in fact about 10 amino acids make up the
active site.
The secondary structure shown below is an example of a(n):
Answer
Parallel beta sheet
Staphylokinase is said to be a dimer. What is a dimer? Structurally a dimer describes
what level of protein structure?
Answer
A dimer contains two polypeptide chains interacting covalently. This describes the
quaternary structure which has two or more polypeptide chains.
Why are proteins the most important macromolecule?
Answer
They perform most of the work in cells.
How many different proteins are found in humans?
Answer
At least 20,000 different proteins
What are some functions of proteins?
Transport
Hormones
Catalysis
Structure
Protection
Answer
Transport
Proteins help to move molecules around the cell and organism.
i.e. hemoglobin - blood based protein that carries oxygen from the lungs to the tissues
Hormones
these molecules communicate messages between cells
i.e. relaxin - a protein that helps women during childbirth by relaxing pelvic ligaments to
make delivery easier
Catalysis (proteins also known as enzymes)
speed up chemical reactions
i.e. protease - breaks down proteins in cells and help organisms recycle unneeded
proteins; also added to laundry detergent to degrade stains with protein (blood, food)
Structure
give strength to cells, organelles, and tissues
i.e. collagen - found in cartilage, skin, and tendons
Protection
ability to fight foreign invaders (outside proteins and toxins)
i.e. antibodies
Amino acids
monomers used as building blocks
contain both an amine functional group and a carboxylic acid functional group; both
functional groups are connected to an alpha carbon
What permits all amino acids to link together in a protein?
each amino acid has the same HN3, CH, COO- groups
What makes amino acids unique?
the unique part of each amino acid is indicated by the R, which is called the side chain
side chains differ in composition, size, and charge
while each amino acid has a different side chain, they can be classified by their
commonality in structure
its is common to group the side chains by charge, size, and polarity
True or False: All proteins are constructed from the same 20 amino acids
True
What is physiological pH?
7.4
Non-polar aliphatic (straight chain amino acids)
relatively small - permits them to interact with other groups
found in the interior of the protein, away from water, nestled with other aliphatic groups
*Proline is a unique amino acid that deviates from the general structure as the side
chain bonds to the backbone N; only amino acid with this type of structure (not flexible -
advantage and disadvantage in protein structure)
Non-polar aromatic group of amino acids
similar to aliphatic in that they are non-polar, but the side chains of these compounds
contain a ring of carbons as an aromatic functional group
more rigid and not as small as the aliphatic group
Polar, but neutral amino acids
contain side chains that have a dipole, and most can H-bond
this permits these amino acids to interact strongly with water and are often found on the
outside of the protein and in contact with water
Acidic amino acids
have side chains with pKa values smaller than 7, which indicates they lose their proton
in the acidic pH range
this property also means that at physiological pH these amino acids are negatively
charged
Basic amino acids
have a pKa that is near or greater than 7, which means their side chains are normally
positively charged
these molecules are often found in contact with water because they H-bond
they are often located near acidic residues in proteins to take advantage of favorable
interactions between positive and negative charges
Histidine
does not have a charged group on its side chain
At a slightly lower pH, it would appear as depicted - the pKa of the side HN+ group
(indicated by the double dagger) is 6.00, so it typically has no charge at pH 7.4
True or False: cysteine is a unique amino acid that is neutral and polar with an
uncharged side chain that can form disulfide bonds by their sulfur atoms covalently
bonding
True
disulfide bonds
stabilize a protein structure when present
not all proteins contain these bonds, but they are common in proteins that exist outside
of the cell
i.e. keratin - protein component of hair; straight or curly hair holds its shape through
disulfide cross linking between strands of hair, these bonds are strong which permits
hair to maintain its shape
polypeptides
long chains of amino acids (99 residues or less)
True or False: As macromolecules, proteins are synthesized from an average of 100 to
300 amino acids into a large chain
True
What dictates the exact sequence of amino acids?
cell's DNA
Where does synthesis of proteins occur?
in the ribosomes, amino acids are covalently linked together to form a protein in a
highly coordinated process
Synthesis reaction of amino acids
the same reaction for each amino acid occurs b/c of the functional groups common to
each amino acid
the amino functional group of one amino acid reacts with the carboxylic acid functional
group of a second resulting in the two monomers joining together to produce a
dipeptide with the release of water --> condensation rxn since one O from the carboxylic
acid group and 2 H from the amino group are lost as water
What kind of bond is formed between two amino acids?
Peptide bond
the ends of the dipeptide formed have reactive amine and carboxylic groups, which
permit them to form additional peptide bonds
peptide/oligopeptide
describes a short chain of amino acids usually from two to twenty amino acids
has an amino-terminal end (N-terminal end) and a carboxylic-terminal end (C-terminal
end)
protein backbone
all the peptide bonds in a protein which link all the amino acids together
residues
term used to refer to the molecule remaining after the condensation rxn takes place
what classifies a molecule as a protein instead of a polypeptide?
100 residues
What is the mass for a protein that has 100 amino acids?
10,000 g/mol (Da - Dalton) or 10 kDa
supramolecular chemistry
the chemistry of large compounds
conformation
3D structure of proteins
biologically active conformational structures
most proteins adopt a conformation that, when folded, is either fibrous or globular
True or False: shape is important to function when adopting a specific conformation.
True
intrinsically disordered
portions of proteins may exist in a random conformation
What are the four standard levels of protein structure?
1. Primary
2. Secondary
3. Tertiary
4. Quaternary
Primary Structure
refers to the order of amino acids covalently bonded together, including disulfide bonds,
in a polypeptide chain
True or False: scientists routinely use the one-letter abbreviations to show amino acid
sequence.
True
i.e. the first 60 amino acids in the sequence for insulin depicted
Scientists write the sequence, starting with the N-terminal amino acid residue on the
left, and continue writing the sequence to the right in the direction of the C-terminal
True or False: proteins contain at least 100 amino acids, but they may contain
thousands of residues in one chain
True
How do scientists write out the sequence of a protein?
Secondary Structure
used to examine the local 3D structure of amino acid residues close in linear sequence;
there are 3 types of secondary structures
(3) beta-turns
Secondary Structure - alpha helices
(1) alpha-helices: coiled structures where the backbone atoms form H-bonds to stabilize
this sequence; standard helix has 3.6 amino acids/residues per each "turn" while rising
5.4 angstroms per turn (1 angstrom = 1x10-10m); interior of helix has no space; side
chains (R groups) point out of the helix so they can interact with water and other
chemical species
Secondary structure - beta-sheets
(2) beta-sheets: repetitive sheet-like structure; zig-zag orientation that puts adjacent
side chain groups as far apart as possible; formed by individual beta-strands that
interact by H-bonding to one another; parallel and anti-parallel
anti-parallel forms when one beta-strand ends and the amino acid sequence turns back
around on itself, then an additional beta-strand can join other strands to form anti
parallel sheets parallel beta-sheets have beta-strands going in the same direction
differences: H-bonding partners are different and the distance of each repeat is unique -
parallel repeats every 6.5A while the anti-parallel repeats every 7.0A
True or False: About 30% of amino acids are found in turns
True
these turns are changes in the direction of the N and C terminals of the primary
sequence
these turns permit proteins to form secondary structures immediately next to one
another
secondary structure - beta turn
a four-residue unit that turns 180 degrees
the turn is seen as a "rope" connecting the two strands
beta-turns can form with both the alpha helix and beta sheet
motif
collection of particularly stable groups of secondary structures
occupy a position b/w secondary and tertiary structures but are not one of the four
levels specified by scientists
i.e. helix-turn-helix composed of an Alpha helix, followed by a turn, and then another
alpha helix
Tertiary structure
the overall 3D structure of the folded polypeptide
non-covalent forces and disulfide bonds maintain tertiary structure in the proper
conformation necessary for function
i.e. myoglobin depicted is critical for our muscle cells for binding and storing O2
prosthetic group
a non-amino acid portion of the molecule necessary for the structure and function of the
protein
fibrous protein
exists in a long, extended structure of alpha helices
quaternary structure
describes macromolecules that have two or more independent polypeptide chains
associated with one another, the number and orientation of these independent chains
constitute the quaternary structure
i.e. staphylokinase, hemoglobin
Dimer
two polypeptides (two subunits)
tetramer
protein with 4 subunits
-in ending
used for proteins that are not enzymes
i.e. hemoglobin, myoglobin
-ase ending
used for proteins that are enzymes
i.e. protease, staphylokinase
enzymes
proteins that accelerate/speed up chemical reactions
have a high specificity for one molecule, or a collection of molecules, due to their
structure (conformation)
How to enzymes speed up chemical reactions?
reactants bind to the enzyme, primarily in the interior, and then undergo a chemical
transformation
this binding helps to speed the reaction along by lowering the energy needed to get the
reaction started
enzymes do this better than inorganic catalysts due to their complementary structure
the result is that reactions speed up 1000 times or more compared to the rate of
uncatalyzed reactions
substrate
the chemical species that bind to the enzyme and are converted to another compound
lyase
catalyze the forming or breaking of double bonds
oxidoreductases
catalyze oxidation and reduction reactions
i.e. luciferase found in lightning bugs
transferals
catalyze the transfer of a group from one molecule to a second
hydrolases
catalyze the breaking, or hydrolysis, of bonds
isomerases
catalyze the rearrangement within a single molecule
ligases
catalyze the joining of two molecules, or two parts of a molecule
How many classes of enzymes exist?
6
co-factor
non-protein components that are critical for activity
i.e. metal ions such as fumerase requires Mg2+ for activity
coenzymes
organic compounds that function as cofactors; aid enzymes by assisting in the transfer
of chemical groups from one compound to a second
i.e. Vit C, niacin
apoenzyme
an enzyme without the cofactor (either ion or coenzyme)
holoenzyme
when the cofactor is added to the apoenzyme to produce a functional enzyme
active site
specific spot on the enzyme where catalysis takes place
composed of 10 amino acids that form non-covalent interactions with the substrate
which helps to generate a favorable energy change to enhance the reaction
induced fit
small movements of the amino acids in the enzyme to bind specifically to the substrate
interactions at the active site of the enzyme that provide energy to change the
conformation of the enzyme to accommodate the substrate
transition state
the structure of the molecule in its transition into a new molecule
most unstable part of the reaction d/t high potential energy
true or false: increasing the concentration of enzyme generally increases the rate of the
reaction
true
True or False: unfolding renders the enzyme inactive, which means it does not catalyze a
reaction
True
What is the optimal temperature for human function?
37 degrees celsius
inhibitors
slow down or stop enzyme reactions by binding to the enzyme via non-covalent
interactions; reversible inhibitors
1. competitive
2.uncompetitive
3.mixed
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