Chapter 2: Nucleic Acids, Genomics and Proteomics

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Chapter 2 Nucleic Acids, Genomics and Proteomics
ZHOU Yong
Department of Biology Xinjiang Medical University
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Teaching Requirements

• 1. Mastering components and types of
  nucleotides component and structure of DNA.
• 2. Comprehending the types, structures, and
  functions of RNA.
• 3. Understanding start and stop codons.

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Chapter 2 Nucleic Acids, Genomics and Proteomics
A Building Blocks Nucleotides B DNA
Structure C RNA Structure D Genes E
Genomics and Proteomics
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Section A Building Blocks - Nucleotides  A
nucleotide is composed of three parts  pentose,
base and phosphate group.  In DNA or RNA, a
pentose is associated with only one phosphate
group, but a cellular free nucleotide (such as
ATP) may contain more than one phosphate group. 
If all phosphate groups are removed, a nucleotide
becomes a nucleoside.
The general structure of nucleotides. 
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Pentose
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Bases
Adenine (A), Cytosine (C), Guanine (G), Thymine
(T), and Uracil (U).
Among them, A, C, G and T  exist in DNA A, C, G
and U  exist in RNA. A and G contain a pair of
fused rings, classified as purines.  C, T, and U
contain only one ring, classified as pyrimidines.
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Cellular Nucleotides and Nucleosides
In cells, a free nucleotide may contain one, two
or three phosphate groups.  The energy carrier
ATP (adenosine triphosphate) has three phosphate
groups.
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If all phosphate groups are removed, a nucleotide
becomes a nucleoside.
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The Nucleic Acid Chain
In a nucleic acid chain, two nucleotides are
linked by a phosphodiester bond, which may be
formed by the condensation reaction.
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Orientation of a nucleic acid chain
Its 5' end contains a free phosphate group and 3'
end contains a free hydroxyl group.  Synthesis of
a nucleic acid chain always proceeds from 5' to
3'.  Therefore, unless specified otherwise, the
sequence of a nucleic acid chain is written from
5' to 3' (left to right).
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NOTE
In DNA or RNA, a nucleic acid chain is also
called a strand.  A DNA molecule typically
contains two strands whereas most RNA molecules
contain a single strand. The length of a nucleic
acid chain is represented by the number of
bases.  In the case of a double-stranded nucleic
acid, bases are paired between two strands. 
Therefore, its length is given by the number of
base pairs (bp).  1 kb 1000 bases or bp 1 Mb
1 million bases or bp. Oligonucleotides refer
to short nucleic acid chains (lt 50 bases or bp)
and polynucleotides have longer chains.
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Section B DNA Structure
The two complementary strands of a DNA double
helix run in opposite directions, that is, they
are antiparallel. Two hydrophilic
sugarphosphate backbones lie on the outside of
the molecule, and the purines and pyrimidines lie
on the inside of the molecule. The double helix
makes a turn every ten base pairs (approximately
3.4 nm).
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Adenine (A) always pairs with thymine (T), and
guanine (G) always pairs with cytosine (C).
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NOTE
Due to the specific base pairing, DNA's two
strands are complementary to each other.  Hence,
the nucleotide sequence of one strand determines
the sequence of another strand.  For example, in
Figure 3-B-2, the sequence of the two strands can
be written as 5'
-ACT- 3' 3' -TGA- 5' Note
that they obey the (AT) and (CG) pairing rule. 
If we know the sequence of one strand, we can
deduce the sequence of another strand.  For this
reason, a DNA database needs to store only the
sequence of one strand.  By convention, the
sequence in a DNA database refers to the sequence
of the 5' to 3' strand (left to right). 
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Section C RNA Structure
Most cellular RNA molecules are single stranded. 
They may form secondary structures such as
stem-loop and hairpin.
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Classification of RNA
messenger RNA (mRNA) transfer RNA
(tRNA) ribosomal RNA (rRNA) Ribozyme Small RNA
molecules
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The mRNA-ribosome-tRNA complex formed during
protein synthesis.
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Ribozyme
Ribozymes are the RNA molecules with catalytic
activity.  They were discovered in early 1980s by
Thomas Cech and Sidney Altman who shared the 1989
Nobel Prize in Chemistry.
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Small RNA Molecule
Small RNA molecules in the nucleus are denoted by
snRNA (small nuclear RNA).  One of their
functions is to participate in RNA splicing.  An
snRNA contains 107-210 nucleotides.  In mammals,
six such molecules have been identified,
designated as U1 to U6, since their sequences are
rich in uracil residues.  Small RNA molecules
are also found in the cytoplasm.  For example,
the signal recognition particle (SRP) involved in
protein transport contains an RNA molecule with a
length of 300 nucleotides.
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Section D Genes
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The b-globin gene family includes b, d, Ag, Gg
and e.  Y is a pseudogene.  HS1 to HS4 are
regulatory elements.
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Section F Genomics and Proteomics
"Genome" is the total genetic material of an
organism.  It may also refer to the subset of a
whole genome.  For example, the mitochondrial
genome is the total genetic material in the
mitochondrion.  Without specified otherwise, the
genome size usually means the haploid genome
size.  That is, only one set of chromosomes are
counted.
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Section F Genomics and Proteomics
The word "proteomics" comes from "protein" and
"genomics".  Its goal is to find the structures
and functions of all proteins encoded in the
genome.  Since the human genome is almost
completely sequenced, proteomics will be the
focus of biomedical research in the 21st century. 
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The genomes of prominent organisms
Organism Genome
Size (Mb) Gene Number Hepatitis D virus
0.0017
1 Hepatitis B virus
0.0032
4 HIV-1
0.0092
9 Bacteriophage l
0.0485
 80 Escherichia coli
4.6392 4400 S.
cerevisiae (yeast) 12.155
6300 C. elegans
(nematode) 97
19000 D. melanogaster (fruit
fly) 137
13600 Mus musculus (mouse)
3000 ? Homo
sapiens (human) 3000
30000(?)
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REVIEW QUESTIONS

• All amino acids are characterized as having
• A. a carboxyl group
• B. an amino group
• C. a variable R group
• D. a central alpha carbon
• E. all of the above

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REVIEW QUESTIONS

• 1. What is the difference between DNA and RNA?
• 2. List the four different nucleotides found in
  DNA, the typical Watson-Crick base pairings, and
  the number of hydrogen bonds in each of those
  pairings.