BCEM 393 - Nucleic Acids

Fill in the blank: the sequence of bases uniquely characterizes a nucleic acid and is a form of ____________.

Linear information

Fill in the blanks: the sugar in deoxyribonucleic acid is __________. The prefix refers to the fact that the 2’ carbon atom of the sugar __________ that is _________ in ribose.

Lacks the oxygen atom, present

Fill in the blanks: the sugars in nucleic acids are linked to one another by _____________. Specifically, the 3’-OH group of the sugar component of one nucleotide is bonded to a ____________ group, which is joined to the 5’-OH group of the adjacent sugar, forming a ____________.

Phosphodiester bridges, phosphoryl, phosphodiester linkage

Fill in the blanks: two of the bases are derivatives of purine - _________ and __________ - and two are derivatives of pyrimidine - ___________ and ____________.

Adenine, guanine, cytosine, thymine (or uracil in RNA)

Fill in the blanks: RNA, like DNA, is a long, unbranched polymer consisting of nucleotides joined by ___ → ___ ____________.

3’, 5’, phosphodiester linkages

True or False: each phosphodiester linkage in the backbone of both DNA and RNA has a negative charge, which repels nucleophilic species that can disrupt the integrity of the information stored in nucleic acids.

True

True or False: in the presence of nucleophilic species, a 2’-OH group on DNA would hydrolyze the phosphodiester linkage and cause a break in the nucleic acid backbone.

True

Fill in the blanks: a unit consisting of a base bonded to a sugar, and one or more phosphates is referred to as a ___________.

Nucleotide

Fill in the blank: a unit consisting of a base bonded to a sugar is referred to as a ____________.

Nucleoside

Fill in the blanks: the four nucleoside units in DNA are called _________, __________, _________, and __________.

Deoxyadenosine, deoxyguanosine, deoxycytidine, thymidine

True or False: the thymine nucleoside is called deoxythymidine because it contains a deoxyribose.

False; the thymine nucleoside is called thymidine, because even though it does contain a deoxyribose, thymine-containing nucleotides are found only rarely in RNA.

Fill in the blanks: the four nucleoside units in RNA are called __________, ____________, ___________, and __________.

Adenosine, guanosine, cytidine, uridine

True or False: a nucleotide is a nucleoside joined to one or more phosphoryl groups by an ester linkage and is most commonly referred to as a nucleoside with the number of attached phosphoryl groups notes.

True

Fill in the blank: nucleoside ____________ are the monomers that are linked to form RNA and DNA.

Triphosphates

Fill in the blanks: the four nucleotide units that link to form DNA are nucleoside monophosphates called ___________, ___________, __________, __________. Note that __________ is released when the nucleotides are linked.

Deoxyadenylate, deoxyguanylate, deoxycytidylate, thymidylate, pyrophosphate

Fill in the blanks: in the DNA double helix, adjacent bases are separated by ____ Å (distance from one base to the next along the backbone). The structure repeats along the helical axis (vertical) at intervals of ___ Å, which corresponds to about ____ bases per turn. Looking down the helix axis, there is a rotation of about ___ degrees per base, with a width of ____ Å.

3.4, 34, 10.4, 36, 20

Fill in the blanks: two DNA chains of opposite directionality intertwine to form a ___________ double helix. The strands run in opposite directions; that is, they have opposite _________ or __________. One strand has a 5’ to 3’ direction and the other has a 3’ to 5’ orientation.

Right-handed, directionality, polarity

Fill in the blanks: in DNA, the sugar-phosphate backbones are on the __________ and bases are on the ___________.

Outside, inside

Fill in the blanks: in DNA, the bases are nearly ___________ to the axis of the helix with adjacent bases separated by ____ Å. The helical structure repeats every ___ Å, with about ___ bases per turn. There is a rotation of nearly ____ degrees per base.

Perpendicular, 3.4, 34, 10.4, 36

True or False: the DNA helix is approximately 34 Å wide.

False; the helix is approximately 20 Å wide (the helical structure repeats every 34 Å)

Fill in the blanks: guanine and cytosine are paired by ___ hydrogen bonds, and adenine and thymine are paired by ____ hydrogen bonds.

3, 2

Fill in the blanks: __________ and __________ are paired by 3 hydrogen bonds, and __________ and __________ are paired by 2 hydrogen bonds.

Guanine, cytosine, adenine, thymine

Fill in the blanks: variations in base pairing can occur due to (1) rotation of a base in RNA or DNA ends, referred to as _____________, (2) tautomerization, referred to as ____________, and (3) rotation around C-1’ to N glycosidic bond, referred to as _____________.

Reverse Watson Crick, wobble base pairs, Hoogsteen

Fill in the blanks: the stacking of bases one on top of another contributes to the stability of the DNA double helix in two ways. First, the double helix is stabilized by the ____________. That is, hydrophobic interactions between the bases drive the bases to the interior of the helix resulting in the exposure of the more polar surfaces to the surrounding water. Second, stacked bases attract one another through ____________, a phenomenon called ___________.

Hydrophobic effect, van der Waals forces, base stacking

Fill in the blanks: DNA has two distinct grooves, called the __________ and the __________. These grooves arise because the ____________ of each ___________ are not __________ each other.

Major groove, minor groove, glycosidic bonds, base in a pair, diametrically opposite

Fill in the blanks: each DNA groove is lined by potential ___________ ____________ and ___________ atoms that enable interactions with proteins. These interactions are essential for ___________ and ___________ because particular proteins bind to DNA, recognizing specific ______________ __________ and ___________ on the surfaces of the grooves, to catalyze these processes.

Hydrogen-bond, donor, acceptor, replication, transcription, hydrogen-bond, donors, acceptors

Fill in the blanks: DNA in bacteria must have a very compact shape to fit in the cell. Because of this, the axis of the double helix can itself be twisted into a superhelix in bacteria, a process called ___________.

Supercoiling

True or False: most naturally occurring DNA molecules are negatively supercoiled.

True

Fill in the blanks: most naturally occurring DNA molecules are negatively supercoiled. Negative supercoiling arises from the ___________ or ___________ of the DNA. In essence, negative supercoiling prepares DNA for processes requiring separation of the DNA strands, such as ___________ or ___________. Positive supercoiling condenses DNA as effectively, and it makes strand separation ________ difficult.

Unwinding, underwinding, replication, transcription, more

True or False: negative supercoiling condenses DNA more effectively than positive supercoiling.

False; positive supercoiling condenses DNA as effectively as negative supercoiling

True or False: negative supercoiling makes strand separation more difficult than positive supercoiling.

False; positive supercoiling makes strand separation more difficult than negative supercoiling (this is why negative supercoiling is more prevalent)

True or False: supercoiling is only a property of circular DNA.

False; supercoiling also applies to linear DNA molecules that have a constrained configuration, such as when DNA is packaged into chromosomes

Circular DNA Fun Fact: more than half of human cancer cells contain extrachromosomal circular DNA, and the circles carry genes required for tumor growth. Additionally, normal heart cells have extrachromosomal circular DNA with genes for the muscle protein titin, which is responsible for muscle plasticity. These discoveries open a new way of looking at eukaryotic DNA and the flexibility of the eukaryotic genome.

Circular DNA Fun Fact

Multiple Choice: which species of plasmid (circular piece of DNA) would migrate fastest through an agarose gel during electrophoresis?

a) Relaxed circular

b) Supercoiled

b)

Multiple Choice: DNA is less susceptible than RNA to hydrolysis. Which of the following contributes most to this difference?

a) DNA is double stranded, whereas RNA is single stranded

b) DNA has 2’ hydrogen atoms, whereas RNA has 2’ hydroxyl groups

c) DNA includes thymine bases, whereas RNA includes uracil bases

d) DNA seldom forms non-Watson-Crick base pairs, whereas RNA does so more readily

e) DNA seldom adopts stable tertiary structure folds, whereas RNA does so more readily

b)