UW BIO 200 EXAM 1 QUESTIONS AND ANSWERS
/.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 - Answer-nucleic acid monomer, comprised of a phosphate group on 5' end
and nitrogenous base on 1' end of carbon ring
/.nucleic acid - Answer-
/.phosphodiester linkage - Answer-when 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 - Answer-the DNA chains run in opposite directions (one side going 5'-3'
and the other, 3'-5')
/.3' - Answer-the end of a chain with the hydroxyl group (carbon #6); this is the growing
end
/.5' - Answer-the 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 - Answer-Guanine 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 - Answer-DNA--(transcribed into)-->RNA---
(translated to)--->proteins
/.RNA v. DNA stability - Answer-RNA has an second, relatively-highly-reactive OH-
group
/.AMINO ACIDS - Answer-
,/.chemical evolution - Answer-monomers 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 - Answer-acts as a base
/.carboxyl groups - Answer-eg. carboxylic acids
/.carbonyl groups - Answer-aldehydes especially react to produce larger molecules; has
C=O bond
/.hydroxyl - Answer-(OH group), highly polar, soluble in water, weak acid
/.phosphate - Answer-linked together, these store a lot of potential energy due to the
electrons on the phosphate groups crowding (electron repulsion)
/.sulfhydryl - Answer-thiols; when present in proteins, can form S-S bonds to form
proteins
/.PROTEINS AND ENZYMES - Answer-
/.macromolecule - Answer-a very large molecule made up of smaller molecules joined
together (aka polymers)
/.Why R-groups are important - Answer-They 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 - Answer-proteins that facilitate folding in cells- part of the heat-
shock proteins
/.heat-shock proteins - Answer-produced 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 - Answer-even 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 - Answer-inorganic ions that interact with enzymes
/.coenzymes - Answer-organic molecules that reversibly interact with enzymes, such as
electron carriers NADH or FADH2
, /.prosthetic groups - Answer-non-amino acid atoms/molecules that are permenantly
attached to proteins
/.induced fit - Answer-change in chape of an enzyme that occurs when a substrate
binds to the active site.
/.competitive inhibition - Answer-regulatory molecule inhibits substrates from accessing
the active site
/.allosteric regulation - Answer-another molecule binds on to the enzyme (but not on the
active site), changing its shape so that its function is also changed
/.primary structure - Answer-The sequence of amino acids in a protein
/.secondary structure - Answer-Amino-carboxy backbone interactions cause folding in
certain ways (examples of this include a-helices and ß-pleated sheets)
/.tertiarty structure - Answer-R-group interactions cause further folding to contribute to
the overall globular protein shape
/.quaternary structure - Answer-Interactions between 2 or more proteins
/.ligand - Answer-Any molecule that binds to a specific site on a receptor molecule.
/.voltage-gating - Answer-opens as the cell polarizes or depolarizes to a specific voltage
/.activation energy - Answer-energy required for a reaction to occur
/.transition state - Answer-temporary unstable intermediate condition where the degree
of interaction between enzyme and substrate increases and reaches a maximum
/.energetic coupling - Answer-chemical 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 - Answer-a bond between two molecules resulting from an
electrostatic attraction between a proton in one molecule and an electronegative atom in
the other
/.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 - Answer-nucleic acid monomer, comprised of a phosphate group on 5' end
and nitrogenous base on 1' end of carbon ring
/.nucleic acid - Answer-
/.phosphodiester linkage - Answer-when 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 - Answer-the DNA chains run in opposite directions (one side going 5'-3'
and the other, 3'-5')
/.3' - Answer-the end of a chain with the hydroxyl group (carbon #6); this is the growing
end
/.5' - Answer-the 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 - Answer-Guanine 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 - Answer-DNA--(transcribed into)-->RNA---
(translated to)--->proteins
/.RNA v. DNA stability - Answer-RNA has an second, relatively-highly-reactive OH-
group
/.AMINO ACIDS - Answer-
,/.chemical evolution - Answer-monomers 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 - Answer-acts as a base
/.carboxyl groups - Answer-eg. carboxylic acids
/.carbonyl groups - Answer-aldehydes especially react to produce larger molecules; has
C=O bond
/.hydroxyl - Answer-(OH group), highly polar, soluble in water, weak acid
/.phosphate - Answer-linked together, these store a lot of potential energy due to the
electrons on the phosphate groups crowding (electron repulsion)
/.sulfhydryl - Answer-thiols; when present in proteins, can form S-S bonds to form
proteins
/.PROTEINS AND ENZYMES - Answer-
/.macromolecule - Answer-a very large molecule made up of smaller molecules joined
together (aka polymers)
/.Why R-groups are important - Answer-They 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 - Answer-proteins that facilitate folding in cells- part of the heat-
shock proteins
/.heat-shock proteins - Answer-produced 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 - Answer-even 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 - Answer-inorganic ions that interact with enzymes
/.coenzymes - Answer-organic molecules that reversibly interact with enzymes, such as
electron carriers NADH or FADH2
, /.prosthetic groups - Answer-non-amino acid atoms/molecules that are permenantly
attached to proteins
/.induced fit - Answer-change in chape of an enzyme that occurs when a substrate
binds to the active site.
/.competitive inhibition - Answer-regulatory molecule inhibits substrates from accessing
the active site
/.allosteric regulation - Answer-another molecule binds on to the enzyme (but not on the
active site), changing its shape so that its function is also changed
/.primary structure - Answer-The sequence of amino acids in a protein
/.secondary structure - Answer-Amino-carboxy backbone interactions cause folding in
certain ways (examples of this include a-helices and ß-pleated sheets)
/.tertiarty structure - Answer-R-group interactions cause further folding to contribute to
the overall globular protein shape
/.quaternary structure - Answer-Interactions between 2 or more proteins
/.ligand - Answer-Any molecule that binds to a specific site on a receptor molecule.
/.voltage-gating - Answer-opens as the cell polarizes or depolarizes to a specific voltage
/.activation energy - Answer-energy required for a reaction to occur
/.transition state - Answer-temporary unstable intermediate condition where the degree
of interaction between enzyme and substrate increases and reaches a maximum
/.energetic coupling - Answer-chemical 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 - Answer-a bond between two molecules resulting from an
electrostatic attraction between a proton in one molecule and an electronegative atom in
the other
