2nd OA Dump File
Green= questions or things on 2nd OA
** NOT SURE IF ALL THESE ANSWERS ARE CORRECT, THESE ARE
WHAT I USED AND PASSED
UNIT 2: AMINO ACIDS, PEPTIDE BONDS, PROTEIN STRUCTURE
• Remembering amino acids
o Polar amino acids- Polar bears like water! Polar amino acids = OH, NH, SH or use S.O.N
o Nonpolar amino acids- hydrophobic- CH “Can’t Have” water - Question w/ pics of
amino acids where you pick out the non-polar (CH) amino acid
Look for CH, CH2, CH3 these are weak interactions that tend to go in the middle
of a protein (aggregation) and are affected by temperature change.
o Ionized amino acids- the charged amino acids +/- attached to them.
Neurodegenerative protein aggregation: Misfolding of a protein structure in Alzheimer’s
Disease the most common neurodegenerative disease. The formation of the aggregated
amyloid-beta fibers another characteristic of Alzheimer’s. The neurodegeneration and
memory loss can be detected before the amyloid fibers accumulate in the brain.
o Caused by intracellular tangles and extracellular plaques (senile plaques) caused by
ABNORMAL PROTEIN AGGREGATION.
• Chaperones- molecules that help denatured proteins in folding (they help newly
formed proteins and can also help the misfolded ones)
Know the levels of protein structure
Primary= chain of amino acids, peptide bonds forming a polypeptide chain. Covalent
bond= strong and does not denature - What structure would be unaffected by complete
denaturation of multisubunit? Primary!!!! Peptide bonds are strong and covalent.
Primary formed by peptide bonds
Secondary= alpha helix and beta sheets, held together hydrogen bond, denatured by
salt and pH change. Carboxyl grp and amino grp. secondary held together by hydrogen
bonds. Hydrogen bonds formed from 2 polar amino acids!!!
Which factor is most influential in the formation of a protein’s secondary structure?
The formation of hydrogen bonds between amino acids
Tertiary= 3-D shape (sickle cell, arthritis, hemophilia) Changes seen with ↑temp, salt, change in
pH, and reducing agents. Tertiary structure is HYDROPHOBIC, found on inside, protein structure
is stabilized primarily by the hydrophobic effect, disruption of the hydrophobic effect is the
simplest way to denature—which is done by ↑temp from heating up.
Quaternary subunit= more than one polypeptide, HgB Changes seen with ↑temp
, 1. Peptide bond- peptide bonds form between 2 amino acids via DEHYDRATION reaction. During
the reaction, a water molecule (H20) forms from the oxygen of a carboxyl grp and 2 hydrogens
from an amino grp. As water forms, the carbon atom of the carboxyl grp and the nitrogen atom
of the amino grp become bonded together. This bond between the two amino acids is called a
peptide bond. Which molecule is produced when two amino acids are joined by a peptide
bond?
UNIT 3: ENZYMOLOGY AND CATALYTIC MECHANISM
1. There is a question about methotrexate treatment in cancer, I think the question wanted to
know how it affects enzyme activity-----methotrexate works by blocking an enzyme process
in
cancer cells so that they cannot grow (The enzyme dihydrofolate reductase catalyzes a step-in
nucleotide synthesis from folic acid. The medication methotrexate has a similar structure as
folic acid and is used as a chemotherapy agent to inhibit cancer growth. What effect does
methotrexate treatment have?) It binds to folic acid causing substrate level inhibition
dihydrofolate reductase.. (Don’t knowi= if this answer is correct but I chose this.)
2. Induced fit: The substrate and active site are somewhat complementary prior to the
substrate binding; many enzymes will adjust their active site conformation slightly as the
substrate binds to improve the fit. This is known as induced fit. When the molecule is
recognized as the substrate, the enzyme will adjust to form itself around the substrate more
tightly to facilitate a reaction catalyzes.
• Know about substrate enzyme complex- like lock and key
o Each substrate binds to an active site, this produces the enzyme-substrate complex.
This geometrical design depends on noncovalent forces.
o Which region describes the active state of an
enzyme? Region of a substrate that is changed by an
enzyme
Green= questions or things on 2nd OA
** NOT SURE IF ALL THESE ANSWERS ARE CORRECT, THESE ARE
WHAT I USED AND PASSED
UNIT 2: AMINO ACIDS, PEPTIDE BONDS, PROTEIN STRUCTURE
• Remembering amino acids
o Polar amino acids- Polar bears like water! Polar amino acids = OH, NH, SH or use S.O.N
o Nonpolar amino acids- hydrophobic- CH “Can’t Have” water - Question w/ pics of
amino acids where you pick out the non-polar (CH) amino acid
Look for CH, CH2, CH3 these are weak interactions that tend to go in the middle
of a protein (aggregation) and are affected by temperature change.
o Ionized amino acids- the charged amino acids +/- attached to them.
Neurodegenerative protein aggregation: Misfolding of a protein structure in Alzheimer’s
Disease the most common neurodegenerative disease. The formation of the aggregated
amyloid-beta fibers another characteristic of Alzheimer’s. The neurodegeneration and
memory loss can be detected before the amyloid fibers accumulate in the brain.
o Caused by intracellular tangles and extracellular plaques (senile plaques) caused by
ABNORMAL PROTEIN AGGREGATION.
• Chaperones- molecules that help denatured proteins in folding (they help newly
formed proteins and can also help the misfolded ones)
Know the levels of protein structure
Primary= chain of amino acids, peptide bonds forming a polypeptide chain. Covalent
bond= strong and does not denature - What structure would be unaffected by complete
denaturation of multisubunit? Primary!!!! Peptide bonds are strong and covalent.
Primary formed by peptide bonds
Secondary= alpha helix and beta sheets, held together hydrogen bond, denatured by
salt and pH change. Carboxyl grp and amino grp. secondary held together by hydrogen
bonds. Hydrogen bonds formed from 2 polar amino acids!!!
Which factor is most influential in the formation of a protein’s secondary structure?
The formation of hydrogen bonds between amino acids
Tertiary= 3-D shape (sickle cell, arthritis, hemophilia) Changes seen with ↑temp, salt, change in
pH, and reducing agents. Tertiary structure is HYDROPHOBIC, found on inside, protein structure
is stabilized primarily by the hydrophobic effect, disruption of the hydrophobic effect is the
simplest way to denature—which is done by ↑temp from heating up.
Quaternary subunit= more than one polypeptide, HgB Changes seen with ↑temp
, 1. Peptide bond- peptide bonds form between 2 amino acids via DEHYDRATION reaction. During
the reaction, a water molecule (H20) forms from the oxygen of a carboxyl grp and 2 hydrogens
from an amino grp. As water forms, the carbon atom of the carboxyl grp and the nitrogen atom
of the amino grp become bonded together. This bond between the two amino acids is called a
peptide bond. Which molecule is produced when two amino acids are joined by a peptide
bond?
UNIT 3: ENZYMOLOGY AND CATALYTIC MECHANISM
1. There is a question about methotrexate treatment in cancer, I think the question wanted to
know how it affects enzyme activity-----methotrexate works by blocking an enzyme process
in
cancer cells so that they cannot grow (The enzyme dihydrofolate reductase catalyzes a step-in
nucleotide synthesis from folic acid. The medication methotrexate has a similar structure as
folic acid and is used as a chemotherapy agent to inhibit cancer growth. What effect does
methotrexate treatment have?) It binds to folic acid causing substrate level inhibition
dihydrofolate reductase.. (Don’t knowi= if this answer is correct but I chose this.)
2. Induced fit: The substrate and active site are somewhat complementary prior to the
substrate binding; many enzymes will adjust their active site conformation slightly as the
substrate binds to improve the fit. This is known as induced fit. When the molecule is
recognized as the substrate, the enzyme will adjust to form itself around the substrate more
tightly to facilitate a reaction catalyzes.
• Know about substrate enzyme complex- like lock and key
o Each substrate binds to an active site, this produces the enzyme-substrate complex.
This geometrical design depends on noncovalent forces.
o Which region describes the active state of an
enzyme? Region of a substrate that is changed by an
enzyme
