CHE 350 Lecture Notes - Lecture 10: Base Pair, Glycosidic Bond, Uracil
1 | Nucleotides
There are 8 common varieties of nucleotides, each composed of a nitrogenous base linked
to a sugar to which at least one phosphate group is also attached
Bases of nucleotides are planar, aromatic, heterocyclic molecules that are structural
derivatives of either purine or pyrimidine
o
PURINES = Adenine (A) and Guanine (G)
PRYIMIDINES = Cytosine (C), Uracil (U), and Thymine (T)
o
Purines form bonds to a five-carbon sugar (pentose) via their N9 atoms
Pyrimidines bond to pentose through their N1 atoms
When phosphate group is absent, compound is known as nucleoside
2 | Introduction to Nucleic Acid Structure
Phosphates of these polynucleotides are acidic, so at physio pH nucleic acids are
polyanions
Linkage b/w individual nucleosides = phosphodiester bond
oPhosphate is esterified to two ribose units
5’ end = terminal residue whose C5’ is not linked to another nucleotide (has phosphate
sticking out)
3’ end = terminal residue whose C3’ is not linked to another nucleotide
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DNA written left to right, 5’ 3’
Chargaff’s Rule
oA = T
oG = C
Watson-Crick Model of DNA has the following major features:
oTwo polynucleotide chains wind around a common axis to form a double helix
oThe two strands of DNA are antiparallel, but each forms a right-handed helix
oThe bases occupy the core of the helix and sugar-phosphate backbone (chains) run
along the periphery, thereby minimizing the repulsions b/w charged phosphate
groups. The surface of the double helix contains two grooves of unequal length-
major and minor grooves
oEach base is H bonded to a base in the opposite strand to form a planar base pair
(complementary base pairing)
A – T (2 H bonds)
G – C (3 H bonds)
Most DNA molecules are large
oGenome = unique DNA content, allocated among several chromosomes each of
which contains a separate DNA molecule
oMany organisms are diploid = 2 equivalent sets of chromosomes, one from each
parent
oTheir content of unique (haploid) DNA is half their total DNA
Humans = diploid, carry 46 chromosomes per cell; haploid # = 23
RNA is a single-stranded nucleic acid
oReplaces Thymine (T) with Uracil (U)
oBase pairing occurs intramolecularly, giving rise to stem-loop structures
3 | Overview of Nucleic Acid Function
DNA carries genetic info
oDouble strandedness nature of DNA facilitates its replication
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Genes direct protein synthesis
oDNA –transcription mRNA, tRNA reads, makes aminos in translation (THIS
HAPPENS IN THE RIBOSOME proteins
oThe DNA of a gene is transcribed to produce an RNA molecule that is
complementary to the DNA. The RNA sequence is then translated into the
corresponding sequence of amino acids to form a protein
oCentral dogma!!!
4 | Nucleic Acid Sequencing
The overall strategy for sequencing any polymer of nonidentical units:
o1) Cleave the polymer into fragments that are small enough to be fully sequenced
o2) Determine the sequence of residues in each fragment
o3) Determine the order of the fragments in the original polymer by aligning
fragments that contain overlapping sequences
A – Restriction Endonucleases Cleave DNA at Specific Sequences
Modification methylase = enzyme that allows for the addition of a methyl group on DNA
Restriction endonuclease = recognizes the same nucleotide sequence as does the
methylase, cleaves any DNA that has not been modified on at least one of its two strands
oEndonuclease = cleaves a nucleic acid within the polynucleotide strand
oExonuclease = cleaves a nucleic acid by removing one of its terminal residues
This system destroys foreign (phage) DNA containing a recognition site that has not been
modified by methylation
Type II restriction endonucleases = useful in lab
oCleave DNA within the four-to eight-base sequence that is recognized by their
corresponding modification methylase
oMost Type II restriction endonucleases recognize and cleave palindromic DNA
sequences
oMost restriction enzymes cleave the two strands of DNA at positions that are
staggered, producing DNA fragments w/ complementary single strand expression
= sticky ends = Restriction fragments with these can associate by base pairing
with other restriction fragments generated by the same restriction enzyme.
oSome restriction endonucleases cleave the two strands of DNA at the symmetry
axis to yield restriction fragments with fully base-paired blunt ends
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Document Summary
There are 8 common varieties of nucleotides, each composed of a nitrogenous base linked to a sugar to which at least one phosphate group is also attached. Bases of nucleotides are planar, aromatic, heterocyclic molecules that are structural derivatives of either purine or pyrimidine o. Pryimidines = cytosine (c), uracil (u), and thymine (t) o. Purines form bonds to a five-carbon sugar (pentose) via their n9 atoms. Pyrimidines bond to pentose through their n1 atoms. When phosphate group is absent, compound is known as nucleoside. Phosphates of these polynucleotides are acidic, so at physio ph nucleic acids are polyanions. Linkage b/w individual nucleosides = phosphodiester bond: phosphate is esterified to two ribose units. 5" end = terminal residue whose c5" is not linked to another nucleotide (has phosphate sticking out) 3" end = terminal residue whose c3" is not linked to another nucleotide. Dna written left to right, 5" 3". Chargaff"s rule: a = t, g = c.
