Harvey Lodish • Arnold Berk • Paul Matsudaira •
Chris A. Kaiser • Monty Krieger • Matthew P. Scott •
Lawrence Zipursky • James Darnell
Molecular Cell Biology
Fifth Edition
Chapter 4:
Basic Molecular Genetic Mechanisms
Copyright © 2004 by W. H. Freeman & Company
Nucleic acid (macro-molecules):
Determining the correct order amino
acids sequence → structure and
function
Gene (DNA) contains all information
→ build the cells and tissues of
organism
Deoxyribonucleic acid (DNA) contains the
information prescribing the amino acid
sequence of proteins
This information is arranged in units termed
genes
Electron micrograph of DNA
Transcribed into RNA
DNA
Ribonucleic acid (RNA) serves in the cellular machinery that
chooses and links amino acids in the correct sequence
The central dogma: DNA ⌫ RNA ⌫ Protein
DNA and RNA are polymers of nucleotide subunits
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Four basic molecular genetic processes:
Protein synthesis: 1 to 3
rRNA: ribosomal RNA;
tRNA: transfer RNA
rNTPS: ribonucleoside triphosphate monomers;
dNTP:deoxyribonucleoside triphophate
Chemical structure of the principal bases (ch3)
DNA: ATCG
RNA: AUCG
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Structure of nucleic acid
A nucleic acid strand is a linear polymer with end to end directionality
Nucleotide subunits are linked together by phosphodiester bonds
REMEMBER:
DNA = deoxyribonucleotides;
RNA = ribonucleotides (OH-groups at
the 2’ position)
Note the directionality of DNA (5’-3’ & 3’5’) or RNA (5’-3’)
DNA = A, G, C, T ; RNA = A, G, C, U
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Native DNA is a double helix of complementary antiparallel
strands
1953, Watson and Francis: proposed
that DNA has a double-helical
structure Nature, 4356, 737-728 (1953)
DNA consists of two associated
polynucleotide strands that wind
together to form a double helix.
5’→3’; 3’→5’ antiparallel
Base pair: H-bond formation, A-T (2)
and G-C (3)
Complementary: two polynucleotide
consequence of the size, shape and
chemical composition, by base pair
interaction (A-T and C-G)
There are two major forces that
contribute to stability of helix formation:
Hydrogen bonding in base-pairing
Hydrophobic interactions in base
stacking (堆)
Nucleic acid as hetero-polymers
Nucleosides, nucleotides
DNA and RNA strands
(Ribose sugar, (2’-deoxy ribose sugar,
RNA precursor)
DNA precursor)
REMEMBER:
(2’-deoxy thymidine triphosphate, nucleotide)
DNA = deoxyribonucleotides;
RNA =ribonucleotides (OH-groups at the 2’ position)
Note the directionality of DNA (5’-3’ & 3’-5’) or
RNA (5’-3’)
DNA = A, G, C, T ; RNA = A, G, C, U
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So …
DNA
RNA
Most DNA in cells is a right handed
helix
X-ray data of DNA: (B-form)
1.The stacked bases are regularly
spaced 0.34-0.36nm
2.Helix makes a complete turn every
3.6nm, about 10.5 pairs per turn.
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B DNA most common d(CGCGAATTCGCG)•d(CGCGAATTCGCG)
A DNA, in low humidity condition, B transform to A form; RNA-RNA,
RNA-DNA d(AGCTTGCCTTGAG)•d(CTCAAGGCAAGCT)
Z DNA, short DNA molecules composed of alternating purine-pyrimidine
nucleotides (GC), right transform to left
d(CGCGCGCGCGCG)•d(CGCGCGCGCGCG)
B-DNA
A-DNA
Z-DNA
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B-DNA
A-DNA
R.H. helix
R.H. helix
Z-DNA
L.H. helix
DNA compositional biases
Base compositions of genomes: G+C (and therefore also
A+T) content varies between different genomes
The GC-content is sometimes used to classify organism in
taxonomy
High G+C content bacteria: Actinobacteria
e.g. in Streptomyces coelicolor it is 72%
鏈黴菌
Low G+C content: Plasmodium falciparum (~20%)
瘧原虫
Other examples:
Saccharomyces cerevisiae (yeast)
38%
Arabidopsis thaliana (plant)
36%
Escherichia coli (bacteria)
50%
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TBP protein can
binds to the minor
groove of specific
DNA (rich AT)→
untwisting and
sharply bending
the double helix →
transcription
ability ↑
Why is rich AT region ?
DNA can undergo reversible strand separation (denaturation)
Tm: melting temperature
G-C more → need more energy
Denature of single stranded DNA → random coil (without organized structure)
Renature vs hybribization
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Many prokaryotic genomic DNA
and viral DNA are circular
molecules.
Circular DNA molecules in
eukaryotic mitochondria and
chloroplasts
Circular DNA without end, when
replication: open DNA →
unwinding DNA → torsional
stress → winding → formed
super-coil
Topoisomerase I (bacterial and
eukaryotic cell has) → bind to
DNA
→ breaks a phosphodiester bond in one strands DNA formed nick → loss
supercoiled → ligates the two ends of the broken strand.
Topoisomerase II, breaks two strands DNA
Supercoils
Supercoiling of DNA can only occur in
closed-circular DNA or linear DNA where
the ends are fixed.
Underwinding produces negative supercoils,
whereas overwinding produces positive supercoils.
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Supercoiling induced by separating the strands
of duplex DNA (eg., during DNA replication)
DNA (double strain) → open → single strain → replication or transcription→
spuercoiling → need topoisomerase
Relaxed and supercoiled plasmid DNAs
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Different types of RNA exhibit various conformations related
their functions
AUCG: CG has 3 H-bond
Most RNA are single strand
Various RNA → carry out specific functions
Eukaryotic cell, RNA self-splicing
5-10 nucleotides
>10 nucleotides
Three Different Classes of RNA
1) rRNA (ribosomal)
• large (long) RNA molecules
• structural and functional components of ribosomes
• highly abundant
2) mRNA (messenger)
• typically small (short)
• encode proteins
• multiple types, not abundant
3) tRNA (transfer) and small ribosomal RNAs
• very small
• Important in translation
Not all genes encode proteins
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DNA
RNA
Deoxyribonucleic acid
ATCG
Ribonucleic acid
AUCG
More rigid
More stable
More flexible
More unstable
mRNA, rRNA, tRNA
Transcription of protein-coding genes and formation of functional mRNA
DNA → RNA → Protein → function
ATCG
AUCG
mRNA
tRNA
rRNA
Encode:
AA
protein –coding gene
gene → mRNA → protein
DNA replication Direction 5’ to 3’ ~800 nd/sec
RNA polymeration: Direction 5’ to 3’ ~40 nd/sec
Translation Direction 5’ to 3’ ~15 aa/sec
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DNA
transcription
RNA
A template DNA strand is transcribed into a
complementary RNA chain by RNA.
Ribonucleoside triphosphate (rNTP) are polymerized to
form a complementary RNA by RNA polymerase.
Polymerization involves a nucleophilic attack by the 3’
oxygen in the growing RNA chain on the a
phosphate of the next nucleotide → formed
phosphodiester bond and release pyrophosphate
Direction: 5’→ 3’; opposite in polarity to their template
DNA strands
DNA A→U T→A C→ G G→C transcribed to
RNA
Release PPi
RNA polymerase begins transcription is +1
Downstream: +,
Upstream: -
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Bacterial (Prokaryotic) Transcription
Promoters
- DNA sequences that guide RNA polymerase to the beginning of
a gene (transcription initiation site).
Terminators
- DNA sequences that specify then termination of RNA synthesis
and release of RNAP from the DNA.
RNA Polymerase (RNAP)
- Enzyme for synthesis of RNA.
Reaction (ordered series of steps)
1) Initiation.
2) Elongation.
3) Termination.
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