IB BIO I
Proteins/Enzymes/Nucleic Acids
Van Roekel
Test Review – Proteins, Enzymes, Nucleic Acids
Proteins
What are the building blocks of Proteins? Draw and annotate a simple diagram of this molecule.
Amino Acids, composed of an amino group, a carboxyl group, an R group, and a carbon and hydrogen.
How many different kinds of Amino Acids are there? 20 used in protein production
What are the different types of Amino Acids and how are these determined?
Polar – partially charged “R” groups that are composed of electronegative elements (Oxygen, Nitrogen)
and are hydrophilic
Non-Polar – neutral “R” groups that are composed mostly of carbon and hydrogen and are hydrophobic
Electrically Charged – Acidic (Negatively charged) and Basic (Positively Charged) “R” groups that act as
acids and bases. They are hydrophilic.
How is a protein/polypeptide molecule formed?
Condensation reactions remove water from 2 amino acids and form a peptide bond between the amino
group of one and the carboxyl group of another.
Describe the four levels of protein structure and describe each one’s structure and function.
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Primary: Unique sequence of amino acids (held together by peptide bonds) that are determined
by an organism’s genes. The primary structure determines the remaining three levels of protein
and its shape.
Secondary: Folding and bending of primary structure into coils (alpha helix) and pleats (beta
pleated sheets) that are held together by hydrogen bonds between amino and carboxyl groups.
This structure contributes to the overall shape of the protein.
Tertiary: Folding and bending of secondary structure into 3D shapes (globular) called subunits.
They are held together by multiple bonds (hydrogen, ionic, covalent, disulfide) between “R”
groups. The tertiary structure gives proteins their functional properties, such as the active sites
of enzymes.
Quaternary: Composed of 2 or more subunits held together multiple bonds (hydrogen, ionic,
covalent, etc.) The overall structure of the protein is determined by the combination of multiple
subunits and determines the final functions.
Compare the two types of protein molecules as far as structure, solubility, purpose, and examples.
Globular proteins are 3-dimensional spherical “blobs” that are soluble in water and are typically
functional proteins. These include hemoglobin, enzymes (amylase) and insulin. Fibrous proteins are long
narrow chains of protein molecules that are insoluble in water and are typically structural proteins.
These include keratin, actin, and collagen.
Why is the structure of a protein important? The overall structure of a protein will determine its
function.
IB BIO I
Proteins/Enzymes/Nucleic Acids
Van Roekel
Describe 6 functions of proteins and give an example of a protein that performs each function
Storage – protein molecules store different elements or protein molecules (not the same as energy
storage). Ferritin stores iron in a protein capsule. Albumin store protein molecules in egg whites.
Transport – protein molecules that transport materials through the body. Hemoglobin transports oxygen
through the body in the blood stream.
Regulatory/Hormones – hormonal proteins that regulate different process in the body. Insulin regulates
blood glucose levels.
Movement – Proteins that allow the body to move. Actin and myosin cause muscles to contract and
allow the body to move.
Enzymatic – proteins that catalyze metabolic reactions. Amylase is a digestive enzyme that breaks down
starch.
Structural – proteins that provide structure/support to the body or materials that body uses. Spider silk
is a structural protein. Collagen is found in connective tissues (ligaments, tendons, cartilage) in animals
Immunoglobulins – immune system proteins. Antibodies are used as signals to start an immune
response to help fight bacteria and viruses.
Enzymes
What are enzymes? List 3 examples of enzymes
Proteins that act as enzymatic catalysts and affect most metabolic reactions in the body by lowering the
activation energy.
Lipase – Breaks down lipids
Protease – breaks down protease
Maltase – breaks down maltose
Etc…
Describe what is meant by Enzyme Substrate Specificity?
The specific structure of an enzyme will determine its function. Each enzyme breaks down a specific
molecule/affects a specific reaction. Each enzyme has a specific area called the active site that reacts
with a specific molecule called the substrate. The shape of the substrate and active site will
fit/complement each other. The chemical properties of the substrate and active site attract due to
opposite charges. When the substrate fits, the enzyme weakens the bonds of the substrate and lower
the activation energy.
IB BIO I
Proteins/Enzymes/Nucleic Acids
Van Roekel
Explain how enzymes can be used to treat milk for people who are lactose intolerant and why this would
need to be done.
Lactose is a molecule broken down by the enzyme lactase. People who are lactose intolerant do not
have significant amounts of lactase, so lactose is broken down by bacterial colonies that causes
gastrointestinal distress. One way of treating this is to use lactase on milk before bottling it. This will
break down the lactose molecule into its monomers without losing any nutritional value.
Describe three factors that affect Enzyme Catalyzed reactions and draw a graph to represent each one.
(Describe/draw/understand graph for each)
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Temperature: As temperature increase, the rate of reaction also increases up to a certain point,
called the optimum temperature. Here, the enzyme is reacting as fast as possible and is breaking
down the most substrate. Enzymes have an upper limit temperature that they can function in. If
they surpass this temperature they begin to lose their shape and functions. The enzyme is
denatured.
pH: Each enzyme has a specific pH in which it functions best. If an enzyme is in a solution that
varies too far from this pH, it will no longer react with its substrate. This is because hydrogen
ions (H+) will block the negative charges of the active site in an acidic solution and hydroxide
ions (OH_) will block the positive charges of the active site in a basic solution.
Substrate Concentration: As substrate concentration increase, so will the rate of reaction up to a
certain point. Here, all the active sites of every enzyme is bound to a substrate, so there is a
maximum rate at which enzymes can function. Because every enzyme is working as fast as
possible and every enzyme is bound to a substrate, there is a maximum amount of substrates
that can be broken down at any given point.
Compare the two types of enzyme inhibitors and how they function
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Competitive Inhibitor – these enzymes resemble the enzymes normal substrate and compete for
the active site of the enzyme. Binds to active site and prevents substrate from binding
•
Noncompetitive enzyme (allosteric) – does not enter the active site of the enzyme. It binds
elsewhere on the enzyme (allosteric site) and causes a conformational change, altering active
site and preventing the substrate from binding.
Describe how enzymes use negative feedback mechanisms to inhibit reactions
Metabolic pathways are controlled through negative feedback mechanisms, which occurs when a
product along the metabolic pathway accumulates and signals to the initial enzyme to stop reacting with
initial substrate. Usually uses some type of inhibitor to prevent farther reactions from occurring.
Nucleic Acids
What are nucleic acids? What do they do? Where are they found?
Long chains of nucleotides that serve as chemical links between generations. They pass information
down from generation to generation and dictate the amino acid sequences for proteins. Nucleic acids
are found in every cell of every organism (nucleus in eukaryotic, nucleoid in prokaryotic).
IB BIO I
Proteins/Enzymes/Nucleic Acids
Van Roekel
Describe the structure of a nucleotide (draw and annotate a diagram of a nucleotide)
Each nucleotide has a phosphate group (that joins sugar molecules),
a pentose sugar (deoxyribose-DNA, and ribose-RNA), and a nitrogenous
base (Adenine, Thymine (Uracil in RNA), Cytosine, and Guanine)
How are nucleotides combined to form a nucleic acid?
Nucleotides are linked through condensation reactions, which removes water between the phosphate
group of one nucleotide and the sugar of another, and forms phosphodiester bonds. This forms the
sugar phosphate backbone of DNA structures.
Describe the structure of DNA nucleotides (including the 4 types of nitrogenous bases)
Phosphate group, Deoxyribose sugar, Nitrogenous Base (Adenine, Thymine, Cytosine, and Guanine)
Describe the structure of a DNA molecule and draw a simple structure. (Specifically why is it a double
helix?)
DNA is a double helix. It is composed of two nucleic acid strands that are antiparallel (parallel and run in
opposite directions). They are held together by hydrogen bonds in the middle between two
complementary nitrogenous bases. Think of it as a ladder with sugar-phosphate backbones as sides of
ladder and complementary bases as rungs.
What is meant by complementary base pairing and how does it help form the structure of a DNA
molecule?
Bases that pair together in the middle of a DNA double helix are complementary bases. They will always
bind with each other. Purines (adenine and guanine) will always pair with pyrimidines (thymine and
cytosine). Specifically, Adenine will always pair with Thymine and Guanine will always pair with Cytosine.
The bases are held together by hydrogen bonds.
Describe the structure of an RNA molecule and its nucleotide (including the 4 types of nitrogenous
bases)
RNA nucleotides have a phosphate group, a ribose sugar, and 4 nitrogenous bases (Adenine, Uracil,
Guanine, and Cytosine). RNA is a single stranded molecule.
Compare/Contrast DNA and RNA
DNA has deoxyribose as the pentose sugar, where RNA has ribose. DNA has Thymine as one of the
bases, where RNA has Uracil. DNA is double stranded, RNA is single stranded. Both have phosphate
groups, both have adenine, cytosine, and guanine, both are nucleic acids.
IB BIO I
Proteins/Enzymes/Nucleic Acids
Van Roekel