Exam 1 - BIO 200 - UW
DNA, RNA, ETC. - answer
DNA - answer Deoxyribonucleic Acid; has H instead of OH- group on 2' of the 6-carbon
ring; its double-helix structure allows the hydrophobic nitrogenous bases to face away
from water, and the bases themselves hydrogen bond to each other. DNA is uber stable
RNA - answer
nucleotide - answernucleic acid monomer, comprised of a phosphate group on 5' end
and nitrogenous base on 1' end of carbon ring
nucleic acid - answer
phosphodiester linkage - answerwhen the phosphate group on one nucleotide reacts
with the hydroxyl group on another one. this creates a bond with a phosphorus and two
ester (diester) bonds! funny how that works. (ester means an oxygen bonded to two
other groups)
antiparallel - answerthe DNA chains run in opposite directions (one side going 5'-3' and
the other, 3'-5')
3' - answerthe end of a chain with the hydroxyl group (carbon #6); this is the growing
end
5' - answerthe end of a chain with the phosphate group (carbon #5) Conventionally, it's
written as 5'-3' (DNA/RNA is also synthesized in the direction); this is the terminal end
complementary base-pairs - answerGuanine goes with Cytosine, and Adenine with
thymine. These bases hydrogen bone with each other at the exact right distance (e.g.
two purines would overlap).
central dogma of molecular biology - answerDNA--(transcribed into)-->RNA---(translated
to)--->proteins
RNA v. DNA stability - answerRNA has an second, relatively-highly-reactive OH-group
AMINO ACIDS - answer
chemical evolution - answermonomers in the prebiotic soup polymerized to form larger
and more complex molecules, such as the proteins and other types of macromole- cules
,found in organisms. This is a difficult step, because mono- mers such as amino acids do
not spontaneously self-assemble into macromolecules such as proteins.
amino groups/amines - answeracts as a base
carboxyl groups - answereg. carboxylic acids
carbonyl groups - answeraldehydes especially react to produce larger molecules; has
C=O bond
hydroxyl - answer(OH group), highly polar, soluble in water, weak acid
phosphate - answerlinked together, these store a lot of potential energy due to the
electrons on the phosphate groups crowding (electron repulsion)
sulfhydryl - answerthiols; when present in proteins, can form S-S bonds to form proteins
PROTEINS AND ENZYMES - answer
macromolecule - answera very large molecule made up of smaller molecules joined
together (aka polymers)
Why R-groups are important - answerThey enable tertiary structure - R group
interactions cause further folding (after secondary structures have formed) and
contribute to the overall globular protein shape. Also they are what make each amino
acid different
molecular chaperones - answerproteins that facilitate folding in cells- part of the heat-
shock proteins
heat-shock proteins - answerproduced after cells experience high
temperatures/anything that undos tertiary structure. they bind to hydrophobic patches
that otherwise wouldn't be exposed; allows proteins to re-fold
saturation kinetics - answereven with increased substrate amounts, active sites of
enzymes can only take a certain maximum of substrates in a reaction at the fastest rate
that they can
cofactors - answerinorganic ions that interact with enzymes
coenzymes - answerorganic molecules that reversibly interact with enzymes, such as
electron carriers NADH or FADH2
prosthetic groups - answernon-amino acid atoms/molecules that are permenantly
attached to proteins
, induced fit - answerchange in chape of an enzyme that occurs when a substrate binds
to the active site.
competitive inhibition - answerregulatory molecule inhibits substrates from accessing
the active site
allosteric regulation - answeranother molecule binds on to the enzyme (but not on the
active site), changing its shape so that its function is also changed
primary structure - answerThe sequence of amino acids in a protein
secondary structure - answerAmino-carboxy backbone interactions cause folding in
certain ways (examples of this include a-helices and ß-pleated sheets)
tertiarty structure - answerR-group interactions cause further folding to contribute to the
overall globular protein shape
quaternary structure - answerInteractions between 2 or more proteins
ligand - answerAny molecule that binds to a specific site on a receptor molecule.
voltage-gating - answeropens as the cell polarizes or depolarizes to a specific voltage
activation energy - answerenergy required for a reaction to occur
transition state - answertemporary unstable intermediate condition where the degree of
interaction between enzyme and substrate increases and reaches a maximum
energetic coupling - answerchemical energy released from one reaction allows another
to take place (usually by adding ATP to an otherwise endergonic reaction). This actually
changed the reaction over all. Page 144 shows this pretty well; instead of A and B trying
to react via an endergonic reaction, ATP, A, and B are all reacting (thus, different
reactants make for a different chemical reaction). Also, this process is energetically
favorable because the resulting ADP has less potential energy, making it more stable as
a molecule.
CHEMISTRY TO KNOW... SERIOUSLY - answer
hydrogen bonding - answera bond between two molecules resulting from an
electrostatic attraction between a proton in one molecule and an electronegative atom in
the other
van de waals forces - answertransient attraction between atoms when there is a
tinnnnnny negative charge on one and a tinnnnyyy positive charge on another, which
very slightly and very quickly attract each other. This is possible since electrons are
always moving around in a random manner
DNA, RNA, ETC. - answer
DNA - answer Deoxyribonucleic Acid; has H instead of OH- group on 2' of the 6-carbon
ring; its double-helix structure allows the hydrophobic nitrogenous bases to face away
from water, and the bases themselves hydrogen bond to each other. DNA is uber stable
RNA - answer
nucleotide - answernucleic acid monomer, comprised of a phosphate group on 5' end
and nitrogenous base on 1' end of carbon ring
nucleic acid - answer
phosphodiester linkage - answerwhen the phosphate group on one nucleotide reacts
with the hydroxyl group on another one. this creates a bond with a phosphorus and two
ester (diester) bonds! funny how that works. (ester means an oxygen bonded to two
other groups)
antiparallel - answerthe DNA chains run in opposite directions (one side going 5'-3' and
the other, 3'-5')
3' - answerthe end of a chain with the hydroxyl group (carbon #6); this is the growing
end
5' - answerthe end of a chain with the phosphate group (carbon #5) Conventionally, it's
written as 5'-3' (DNA/RNA is also synthesized in the direction); this is the terminal end
complementary base-pairs - answerGuanine goes with Cytosine, and Adenine with
thymine. These bases hydrogen bone with each other at the exact right distance (e.g.
two purines would overlap).
central dogma of molecular biology - answerDNA--(transcribed into)-->RNA---(translated
to)--->proteins
RNA v. DNA stability - answerRNA has an second, relatively-highly-reactive OH-group
AMINO ACIDS - answer
chemical evolution - answermonomers in the prebiotic soup polymerized to form larger
and more complex molecules, such as the proteins and other types of macromole- cules
,found in organisms. This is a difficult step, because mono- mers such as amino acids do
not spontaneously self-assemble into macromolecules such as proteins.
amino groups/amines - answeracts as a base
carboxyl groups - answereg. carboxylic acids
carbonyl groups - answeraldehydes especially react to produce larger molecules; has
C=O bond
hydroxyl - answer(OH group), highly polar, soluble in water, weak acid
phosphate - answerlinked together, these store a lot of potential energy due to the
electrons on the phosphate groups crowding (electron repulsion)
sulfhydryl - answerthiols; when present in proteins, can form S-S bonds to form proteins
PROTEINS AND ENZYMES - answer
macromolecule - answera very large molecule made up of smaller molecules joined
together (aka polymers)
Why R-groups are important - answerThey enable tertiary structure - R group
interactions cause further folding (after secondary structures have formed) and
contribute to the overall globular protein shape. Also they are what make each amino
acid different
molecular chaperones - answerproteins that facilitate folding in cells- part of the heat-
shock proteins
heat-shock proteins - answerproduced after cells experience high
temperatures/anything that undos tertiary structure. they bind to hydrophobic patches
that otherwise wouldn't be exposed; allows proteins to re-fold
saturation kinetics - answereven with increased substrate amounts, active sites of
enzymes can only take a certain maximum of substrates in a reaction at the fastest rate
that they can
cofactors - answerinorganic ions that interact with enzymes
coenzymes - answerorganic molecules that reversibly interact with enzymes, such as
electron carriers NADH or FADH2
prosthetic groups - answernon-amino acid atoms/molecules that are permenantly
attached to proteins
, induced fit - answerchange in chape of an enzyme that occurs when a substrate binds
to the active site.
competitive inhibition - answerregulatory molecule inhibits substrates from accessing
the active site
allosteric regulation - answeranother molecule binds on to the enzyme (but not on the
active site), changing its shape so that its function is also changed
primary structure - answerThe sequence of amino acids in a protein
secondary structure - answerAmino-carboxy backbone interactions cause folding in
certain ways (examples of this include a-helices and ß-pleated sheets)
tertiarty structure - answerR-group interactions cause further folding to contribute to the
overall globular protein shape
quaternary structure - answerInteractions between 2 or more proteins
ligand - answerAny molecule that binds to a specific site on a receptor molecule.
voltage-gating - answeropens as the cell polarizes or depolarizes to a specific voltage
activation energy - answerenergy required for a reaction to occur
transition state - answertemporary unstable intermediate condition where the degree of
interaction between enzyme and substrate increases and reaches a maximum
energetic coupling - answerchemical energy released from one reaction allows another
to take place (usually by adding ATP to an otherwise endergonic reaction). This actually
changed the reaction over all. Page 144 shows this pretty well; instead of A and B trying
to react via an endergonic reaction, ATP, A, and B are all reacting (thus, different
reactants make for a different chemical reaction). Also, this process is energetically
favorable because the resulting ADP has less potential energy, making it more stable as
a molecule.
CHEMISTRY TO KNOW... SERIOUSLY - answer
hydrogen bonding - answera bond between two molecules resulting from an
electrostatic attraction between a proton in one molecule and an electronegative atom in
the other
van de waals forces - answertransient attraction between atoms when there is a
tinnnnnny negative charge on one and a tinnnnyyy positive charge on another, which
very slightly and very quickly attract each other. This is possible since electrons are
always moving around in a random manner
