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Structure of Molecules

1) Nucleic acids have four levels of structure: primary, secondary, tertiary, and quaternary. The primary structure is the sequence of nucleotides. 2) The secondary structure of DNA is its famous double helix structure formed by base pairing between complementary nucleotides on each strand. 3) DNA can further twist and fold on itself to form a compact tertiary structure.

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59 views5 pages

Structure of Molecules

1) Nucleic acids have four levels of structure: primary, secondary, tertiary, and quaternary. The primary structure is the sequence of nucleotides. 2) The secondary structure of DNA is its famous double helix structure formed by base pairing between complementary nucleotides on each strand. 3) DNA can further twist and fold on itself to form a compact tertiary structure.

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STRUCTURE OF MOLECULES/ COMPOUNDS

Because nucleic acids can form huge polymers that can take many forms, there are several
ways to discuss the structure of nucleic acid. The "nucleic acid structure" can mean something
as simple as the nucleotide sequence in a DNA fragment, or something as complex as the
way the DNA molecule bends and how it interacts with other molecules.

Primary Structure

Nucleotides – the building blocks of nucleic acids, and the “letters” of the genetic “code” – are
made of three components:

COMPONENT 1: A nitrogenous base such as adenine, cytosine, guanine and thymine or uracil.
DNA and RNA each have four possible nitrogenous bases; where DNA uses thymine or "T",
RNA uses uracil or "U" instead of thymine. Each of these four bases has different binding
properties, which ensures that the cell does not "mix" one letter with the other. Thymine and
uracil have almost identical structures and properties, which allows them to perform similar
roles in the two different types of nucleic acids.

COMPONENT 2: A sugar-phosphate backbone, which allows the nitrogenous bases to be


strung together. Each nucleotide’s sugar can link to another nucleotide’s phosphate to become
a single molecule. When many nucleotides are strung together, the angle of this phosphate-
sugar bond most often makes the string into a helix. This is why DNA, which is two-stranded,
naturally takes on the shape of a double helix.

In writing nucleotide sequences for nucleic acids, the convention is to write the nucleotides
(usually using the one-letter abbreviations for the bases, shown in Figure 19.5 "Structure of a
Segment of DNA") starting with the nucleotide having a free phosphate group, which is known
as the 5′ end, and indicate the nucleotides in order. For DNA, a lowercase d is often written in
front of the sequence to indicate that the monomers are deoxyribonucleotides. The final
nucleotide has a free OH group on the 3′ carbon atom and is called the 3′ end. The sequence
of nucleotides in the DNA segment shown in Figure 19.5 "Structure of a Segment of DNA"
would be written 5′-dG-dT-dA-dC-3′, which is often further abbreviated to dGTAC.

Figure 1: "Structure of a Segment of DNA"

SECONDARY STRUCTURE

DNA's secondary structure is a double helix formed on the basis of two complementary
polynucleotide strands by hydrogen bonds in base pairs. Actually, the stronger forces holding
the two strands together are stacking interactions between the bases. These stacking
interactions are stabilized by Van der Waals forces and hydrophobic interactions, and show a
large amount of local structural variability. The two polynucleotide chains form the right hand
double helix with the same rotation around the same common axis. The sugar phosphate
backbones of two polynucleotide chains are located at the outer side of the double helix, while
bases are located at the inner side. There are two grooves in the double helix, which are called
major groove and minor groove based on their relative size. The axial distance between
adjacent base pairs is 0.34nm, and the wheelbase of each helix is 3.4nm. At the University of
Cambridge in 1953, James D. Watson and Francis Crick announced that they had a model for
the secondary structure of DNA. Using information from Chargaff experiments (and other
experiments) and data from X-ray studies of Rosalind Franklin (which involves chemists,
physics and sophisticated mathematics), Watson and Crick have worked with models that
were not different from all of a child's construction and finally, I have come to the conclusion
that the DNA consists of two strands of nucleic acid that are antiparallel to each other, that is,
side by side with the end of a string close to the 3 'of the 5 end of the other addition, as shown
model, the two strands are intertwined to form a double helix, a structure that can be compared
to a spiral staircase, in which the phosphate groups and the sugar (the nucleus of the nucleic
acid polymer) represent the outer edges of the structure ladder. Purine and pyrimidine bases
face within the helix, with always opposite to the cytosine and thymine always opposite
guanine adenine. These pairs of specific bases, complementary said bases are the steps or
pegs in our ladder analogy.

Figure 2: Double Helix DNA


TERTIARY STRUCTURE
On the basis of the double helix, DNA molecules twist the coil further in order to form a super
helix to compress the volume. The resultant is called tertiary structure of DNA. The tertiary
arrangement has large-scale folding taking into consideration into geometrical and steric
constraints. Usually, it includes A-DNA, B-DNA and Z-DNA in space.

DNA STRUCTURE
DNA is the cellular molecule that contains instructions for the performance of all cell
functions. When a cell divides, its DNA is copied and passed from one cell generation to the
next generation. DNA is organized into chromosomes and found within the nucleus of our
cells. It contains the "programmatic instructions" for cellular activities. When organisms
produce offspring, these instructions in are passed down through DNA.DNA commonly
exists as a double stranded molecule with a twisted double helix shape. DNA is composed of
a phosphate-deoxyribose sugar backbone and the four nitrogenous bases: adenine (A),
guanine (G), cytosine (C), and thymine (T). In double stranded DNA, adenine pairs with
thymine (A-T) and guanine pairs with cytosine (G-C).

Figure 3: DNA is composed of a phosphate-deoxyribose sugar backbone and the four


nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T).
RNA STRUCTURE

RNA is essential for the synthesis of proteins. Information contained within the genetic code
is typically passed from DNA to RNA to the resulting proteins. There are several different types
of RNA. Messenger RNA (mRNA) is the RNA transcript or RNA copy of the DNA message
produced during DNA transcription. Messenger RNA is translated to form proteins. Transfer
RNA (tRNA) has a three dimensional shape and is necessary for the translation of mRNA in
protein synthesis. Ribosomal RNA (rRNA) is a component of ribosomes and is also involved
in protein synthesis. MicroRNAs (miRNAs) are small RNAs that help to regulate gene
expression. RNA most commonly exists as a single stranded molecule composed of a
phosphate-ribose sugar backbone and the nitrogenous bases adenine, guanine, cytosine and
uracil (U). When DNA is transcribed into an RNA transcript during DNA transcription, guanine
pairs with cytosine (G-C) and adenine pairs with uracil (A-U).

Figure 4: RNA is composed of a phosphate-ribose sugar backbone and the nitrogenous bases
adenine, guanine, cytosine and uracil (U). Sponk/Wikimedia Common

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