Chapter 24: Nucleic Acid Structure Flashcards
ultimate source of biological information?
Nucleic acids
The shapes and activities of individual cells are, to a large extent, determined by genetic instructions contained in
DNA (or RNA, in some viruses).
According to the central dogma of molecular biology, sequences of nucleotide bases in DNA encode?
the amino acid sequences of proteins.
What are the two kinds of nucleic acids and what do they do?
store information and make it available to the cell.
The structures of DNA and RNA are consistent with what 4 things?
- Genetic information must be stored in a form that is manageable in size and stable over a long period.
- Genetic information must be decoded—often many times—in order to be used. Transcription is the process by which nucleotide sequences in DNA are copied onto RNA so that they can direct protein synthesis, a process known as translation.
- Information contained in DNA or RNA must be accessible to proteins and other nucleic acids. These agents must recognize nucleic acids (in many cases, in a sequence-specific fashion) and bind to them in a way that alters their function.
- The progeny of an organism must be equipped with the same set of instructions as in the parent. Thus, DNA is replicated (an exact copy made) so that each daughter cell receives the same information.
What is the structural difference between thymine and uracil?
The only difference between them is the presence of an extra methyl group in the thymine structure.
Which form of DNA is biologically most common?
B-DNA
Structural features of B-DNA?
- The two antiparallel polynucleotide strands wind in a right-handed manner around a common axis to produce an ∼20-Å-diameter double helix.
- The planes of the nucleotide bases, which form hydrogen-bonded pairs, are nearly perpendicular to the helix axis. In B-DNA, the bases occupy the core of the helix while the sugar–phosphate backbones wind around the outside, forming the major and minor grooves. Only the edges of the base pairs are exposed to solvent.
What accounts for the near perfect symmetry of DNA?
Each base pair has approximately the same width (Fig. 24-1), which accounts for the near-perfect symmetry of the DNA molecule, regardless of base composition. A ∙ T and G ∙ C base pairs are interchangeable: They can replace each other in the double helix without altering the positions of the sugar–phosphate backbones’ C1′ atoms. Likewise, the partners of a Watson–Crick base pair can be switched (i.e., by changing a G ∙ C to a C ∙ G or an A ∙ T to a T ∙ A). In contrast, any other combination of bases would significantly distort the double helix.
how many bp per turn of B DNA and helical twist?
The canonical (ideal) B-DNA helix has 10 base pairs (bp) per turn (a helical twist of 36° per bp) and, since the aromatic bases have van der Waals thicknesses of 3.4 Å and are partially stacked on each other, the helix has a pitch (rise per turn) of 34 Å.
The major structural variants of B-DNA?
A-DNA and Z-DNA
Describe A-DNA
A-DNA’s Base Pairs Are Inclined to the Helix Axis.
Under dehydrating conditions, B-DNA undergoes a reversible conformational change to A-DNA, which forms a wider and flatter right-handed helix than does B-DNA.
Has an an axial hole
A-DNA’s most striking feature, however, is that the planes of its base pairs are tilted 20° with respect to the helix axis. Since the axis does not pass through its base pairs, A-DNA has a deep major groove and a very shallow minor groove; it can be described as a flat ribbon wound around a 6-Å-diameter cylindrical hole.
11bp
Where does A-DNA occur?
A short segment of A-DNA occurs in the active site of DNA polymerase during the replication of DNA
Describe Z-DNA
Z-DNA Forms a Left-Handed Helix.
a deep minor groove, and no discernible major groove.
formed under high salt concentration. Left-handed, 12 base pairs per turn, a pitch of 45 Å.
Describe Z-DNA
Z-DNA Forms a Left-Handed Helix.
a deep minor groove, and no discernible major groove.
Does Z-DNA have a biological function?
-The discovery of Z-DNA–binding proteins strongly suggests that Z-DNA does exist in vivo.
-One Zα domain binds to each strand of Z-DNA via hydrogen bonds and ionic interactions between polar and basic side chains and the sugarphosphate backbone of the DNA; none of the DNA’s bases participate in these associations
-Sequences capable of forming Z-DNA frequently occur near the start of genes, and the reversible conversion of B-DNA to Z-DNA at these sites may play a role in the control of transcription.
Are A:T and G:C base pairs are interchangeable? Why?
Yes, They can replace each other in the double helix without altering the positions of the sugar–phosphate backbones’ C1′ atoms.
This is because each base pair has approximately the same width
In contrast, any other combination of bases would significantly distort the double helix.
The major structural features of three types of DNA
A-DNA and B-DNA are right handed helixes & anti conformation
Z-DNA is left handed helix. Anti for pyrimidines; syn for purines
do the structurally distinct A, B, and Z forms of DNA freely interconvert in vivo?
No, Rather, the transition from one form to another requires unusual physical conditions (e.g., dehydration) or the influence of DNA-binding proteins.
Real DNA molecules deviate from the ideal structures, expand on this. Why is this important for proteins.
X-Ray structures of B-DNA segments reveal that individual residues significantly depart from the average conformation in a sequence-dependent manner.
For example, the helical twist per base pair may range from 26° to 43°.
Each base pair can also deviate from its ideal conformation by rolling or twisting like the blade of a propeller.
Such conformational variation appears to be important for the sequence-specific recognition of DNA by the proteins that process genetic information.
DNA has structural flexibility but the flexibility is limited. Why is DNA flexible?
it is imperative that the molecules be somewhat flexible so that they can be packaged in cells. DNA helices can adopt different degrees of curvature ranging from gentle arcs to sharp bends. The more severe distortions from linearity generally occur in response to the binding of specific proteins.
Conformation of a nucleotide is specified by ?
The six torsion angles of the sugar-phosphate backbone and the torsion angle of the glycosidic bond connecting base and sugar.
Are the six torsion angles of the sugar-phosphate backbone and the torsion angle around the glycosidic bond restricted? Due to what?
Yes, due to internal constraints that restrict their rotational freedom.
Because of non-covalent interactions between the ribose ring and the phosphate groups, and steric interference between residues.
The two most common ribose conformations are known as ?
C3′-endo and C2′-endo
The flexibility of the ribose ring is also limited.
The two most common ribose conformations are known as C3′-endo and C2′-endo; “endo” (Greek: endon, within) indicates that the displaced atom is on the same side of the ring as C5′, whereas “exo” (Greek: exo, out of) indicates displacement toward the opposite side of the ring from C5′.
What are the endo conformations of the DNAs
The flexibility of the ribose ring is also limited.
- B-DNA has the C2’-endo conformation.
- A-DNA has the C3’-endo conformation.
- Z-DNA has C3’-endo of purine nucleotides and C2’-endo of pyrimidine nucleotides.
The rotation of a base around its glycosidic bond (angle χ ) is greatly hindered. Purine residues have two sterically permissible orientations known as the
syn (Greek: with) and anti (Greek: against) conformations
Only the anti conformation of ____ is stable, because?
pyrimidines because in the syn conformation, the sugar residue sterically interferes with the pyrimidine’s C2 substituent.
In most double-helical nucleic acids, all bases are in the _____ conformation, which the exception of?
anti
The exception is Z-DNA (Section 24-1A), in which the alternating pyrimidine and purine residues are anti and syn, respectively (this is one reason why the repeating unit of Z-DNA is a dinucleotide).
The chromosomes of many viruses and bacteria are circular molecules of duplex DNA. These molecules are a result of?
DNA supercoiling.
Describe Supercoiled DNA
Why is it important
Supercoiled DNA molecules are more compact than “relaxed” molecules with the same number of nucleotides.
Supercoiling is important for packaging DNA in cells, and for unwinding DNA during replication and transcription.
