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Nucleotide and Nucleic Acid
Structure
Introduction to Cells & Microscopy
Structural Components of Nucleotides
Base
Sugar
Phosphate
Glycosidic bond
H
NUCLEOTIDE
H
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RNA
DNA
Table 3-1
Nucleic acid – polymer of nucleotides – directionality 5’à3’
When you write a sequence:
ATCG
It is assumed that the 5’-end is
on the left and the 3’-end is on
the right, unless otherwise
labeled.
Phosphodiester bonds
5’-ATCG-3’
3’-GCTA-5’ same molecule
Composition of DNA?
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Chargaff’s Rules
DNA is Double Stranded Helix
http://higheredbcs.wiley.com/legacy/college/voet/0470129301/kinemages/exercise_2.html
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Figure 3-8
Computer-simulated space-filling model of DNA.
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• The crucial piece of evidence for DNA structure
came from X-ray “crystallography.” Wilkins learned
how to purify DNA and make regular fiber patterns.
Rosalind Franklin performed the X-ray diffraction
and deduced there was a helix.
• Francis Crick saw the data at a seminar Wilkins
gave and also deduced there was a helix and the
size parameters.
• James Watson discovered how the
bases went together (complementarity)
using Chargaff rules (A=T, G=C).
• Watson & Crick published their
structure in 1953. Beautiful example of
how structure predicted function.
Video: Computer-simulated space-filling model of DNA.
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SUMMARY
(34 Å)
sugar–phosphate
backbone
(phosphodiester
bonds)
Right-handed, antiparallel, doublestranded helix. With the “base
complementarity,” it explains
genetic material:
• Storage of genetic information
• Replication
• Information retrival
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Central Dogma of Molecular
Biology
Introduction to Cells & Microscopy
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From DNA to Protein: Gene Expression
• Central Dogma: from Genes to Proteins
• Replication of the genes (DNAàDNA)
• Transcribing the information (DNAàRNA)
• Translating the nucleotide sequence into
protein sequence (RNAàProtein)
– The Genetic Code
– Protein Biosynthesis
Central Dogma
The central dogma of molecular biology
Replication
Information Flow
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Replication
DNA replication is semiconservative (Meselson-Stahl Expt)
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DNA Replication
Arthur Kornberg showed that DNA contains
information for its own replication.
He combined in a test tube: DNA, the four
deoxyribonucleoside triphosphates
(dNTPs–monomers), DNA polymerase,
salts (Mg+2), and buffer.
The DNA served as a template for
synthesis of new DNA.
Each New DNA Strand Grows from Its 5´ End to Its 3´ End
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Each New DNA Strand Grows from Its 5´ End to Its 3´ End
ALL polymerases
add nucleotides to
the 3’ end
(Direction is termed 5’ g 3’)
Pyrophosphatase
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Transcription
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Central Dogma
The central dogma of molecular biology
Replication
Messenger RNA
(mRNA)
Transfer RNA
(tRNA)
Ribosomal RNA
(rRNA)
Central Dogma
RNA is key to this process:
• Messenger RNA (mRNA)—carries
copy of a DNA sequence to site of
protein synthesis at the ribosome
• Transfer RNA (tRNA)—carries amino
acids for polypeptide assembly
• Ribosomal RNA (rRNA)—catalyzes
peptide bond formation and provides
structure for the ribosome
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Central Dogma
The central dogma of molecular biology
Replication
Transcription
Messenger RNA
(mRNA)
Transfer RNA
(tRNA)
Ribosomal RNA
(rRNA)
Transcription
Transcription components:
• A DNA template for base pairings—one of the two
strands of DNA
• Nucleoside triphosphates (ATP,GTP,CTP,UTP) as
substrates
• An RNA polymerase enzyme
Transcription process:
• RNA polymerase unwinds DNA about ten base pairs at a
time; reads template in 3’ to 5’ direction, synthesizes RNA
in the 5’ to 3’ direction.
• The RNA transcript is antiparallel to the DNA template
strand, and adds nucleotides to its 3’ end.
• NTPs incorporate NMP and PPi is a product!
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Transcription
• Production of mRNA transcript by RNA polymerase
Transcription: Where to start?
5' Flanking
Coding Region
3'-flanking
prokaryotes
Promoter
eukaryotes
The consensus
sequence for
each element in
human genes (N is
any nucleotide)
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Transcription
Translation
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Central Dogma
The central dogma of molecular biology
Replication
Translation
Messenger RNA
(mRNA)
Transfer RNA
(tRNA)
Ribosomal RNA
(rRNA)
What is the relationship between a DNA sequence and an amino acid sequence?
• The Code
• The Adaptors (tRNA)
• The Ribosome (rRNA + rProteins)
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Translation: The Genetic Code
The genetic code: Specifies which amino
acids will be used to build a protein
Codon: A sequence of three bases—each
codon specifies a particular amino acid.
Start codon: AUG—initiation signal for
translation.
Stop codons: UAA, UAG, UGA—stop
translation and polypeptide is released.
Translation: The Genetic Code
The genetic code is redundant.
The genetic code is universal.
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Translation: tRNA
tRNAs must deliver amino acids
corresponding to each codon
The conformation (three-dimensional shape) of
tRNA results from base pairing (hydrogen
bonding) within the molecule.
3‘-end is the amino-acid attachment site—binds
covalently.
At the other end (middle of the tRNA sequence) is
the Anticodon—site of base pairing with mRNA.
Unique for each species of tRNA.
Translation: tRNA
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Translation: tRNA
Template for mRNA –
read 3’à5’
tRNA
anticodon
N
C
Translation: Ribosome
Ribosome: the workbench—holds
mRNA and charged tRNAs in the
correct positions to allow assembly of
polypeptide chain.
Ribosomes are not specific, they can
make any type of protein.
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Translation: Protein Biosynthesis: Ribosome Structure
Ribosomes have two subunits, large and small. When not active in
translation, the subunits exist separately.
• The small subunit (40S) has one ribosomal RNA (rRNA) (18S) and 33
proteins.
• The large subunit (60S) has three molecules of rRNA (28S, 5.8S, 5S)
and 49 different proteins.
• Ribosomal subunits are held together by ionic and hydrophobic forces
(not covalent bonds) (80S).
Translation: Ribosome
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Translation: Protein Biosynthesis; Elongation
EF-Tu
GTP
Decoding
(GTP hydrolysis)
Peptidyltransferase
Translation: Protein Biosynthesis; Elongation
ELONGATION
Translocation
(GTP hydrolysis)
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Central Dogma
The central dogma of molecular biology
Replication
Animated videos of DNA structure and Central Dogma
(https://wileyassets.s3.amazonaws.com/Voet_Fundamentals_of_Biochemistry_5e_ISBNEPROF12533/media/
Guided_Tour/dnaStructure.html)
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