Chapter 5: Nucleic Acids &
Gene Expression
Chapter 29: Nucleic Acids
Structure
Outline of Chpt 5 & 29
• Nucleotide bases, sugars, phosphate (Chpt 5:sec 1)
• Experiments that lead to the discovery of DNA (Chpt 5:sec 2)
–
–
–
–
Avery, MacLeod, McCarty experiment (1934-1944)
Hershey-Chase experiment (1952)
Chargaff’s rules
Watson-Crick structure (1953)
• Chemical Structure of DNA
– Watson & Crick Structure of DNA (chpt 5 sec 3A)
– Structure of A, B, and Z-DNA (chpt 29 sec 1)
– Sugar-Phosphate chain conformations (Chpt 29 sec 2B)
– Semiconservative replication of DNA (chpt 5 sec 3B)
• Information Transfer Processes
– DNA replication: an Overview (chpt 5 4C)
– RNA synthesis: Transcription (chpt 5 sec 4A)
– Protein Synthesis: Translation (chpt 5 sec 4B)
Structure of nucleic acid bases
and numbering scheme
Modified bases found in nucleic
acid structures
Modified bases found in nucleic
acid structures
Structure of the Purines
(Adenine, Guanine)
Notice not a
double bond
Base attaches
at 9-position
Base attaches
at 9-position
Structure of the Pyrimidines
(Cytosine, Thymine, Uracil)
Base attaches
at 1-position
Base attaches
at 1-position
Nomenclature of Nucleic Acids
Nucleotide- a base, sugar and 5’-phosphate group. The
suffix used for nucleotides is –ylate.
Nucleoside- a base and sugar. The suffix used for a
nucleoside is –osine (for purines) and –ine (for pyrimidines).
Sometimes Phosphate groups are
not 5’ but located on other positions
Nucleic acid chains are always
written in the 5’ to 3’ direction.
Where 5’and 3’ are carbons on
the sugar.
Experiments to prove DNA is
the genetic material
• Oswald Avery, Colin MacLeod, Macyln
McCarty (1944)
– Transforming Principle is DNA
• Alfred Hershey & Martha Chase (1952)
– DNA is essential for production of Progeny
S-type
Virulent
R-type
Non-Virulent
Avery, McCarthy, MacCleod Experiment (1944) demonstrated DNA is the
essential chemical that can transform the character of living organisms
Hershey-Chase experiment demonstrated that
protein was not the genetic material in Viral
DNA infection
Structure of B-Form DNA solved
by Watson-Crick in 1952
Major Groove
Minor Groove
Major Groove
Minor Groove
Many bonds exhibit rotation in
the structure of DNA and RNA
Sugar
pucker
Syn or AntiGlycosidic
bond
Ribose Sugar adopts a
cyclopentane structure
• Because of torsional strain, cyclopentane
adopts a puckered conformation
• Four carbon atoms are in a plane
– The fifth carbon atom is above or below the plane – looks like
an envelope
Ribose sugar can pucker at C-2’
or C-3’ in the plane with C-5’
• Endo- means the pucker is on the same face with
C5’.
• Exo- means the pucker is on the opposite the face
of C5’.
The structure of nucleic acids are
in three major forms
-DNA is mostly B-form, some Z-form
-RNA is mostly A-form
Stability of the double-helical
structure of Nucleic Acids
• Negatively charged phosphates are on the
surface where they have the minimum
repulsion between each other.
• Aromatic bases are stacked on top of each
other where they form vertical hydrophobic
contacts (base stacking interactions).
• Hydrogen bonds from the bases of each
strand help connect each strand to each
other.
Information Transfer
Processes: DNA, RNA and
Protein synthesis
By
Doba Jackson
Information Transfer Processes
DNA Replication: Transfer of genetic
information from one cell to the next. Occurs once
during each cells division cycle.
Transcription: Transfer of genetic information
from DNA to RNA. Most RNA is translated to protein
(mRNA) and some cases RNA is the final product.
Translation: Transfer of genetic information in
mRNA to protein.
Information Transfer: Common Processes
Template: a polymerized macromolecule containing
the information to be transferred in a sequence of
monomers.
Monomers: small molecules capable of being
polymerized sequentially to form a macromolecular
template.
Enzymes (Polymerases, etc.): macromolecules
capable of recognizing the monomers, template and
catalyzing the polymerization to form a new
macromolecule.
Energy: Polymerization is energetically unfavorable
and requires coupling to an energetically favorable
process
DNA is synthesized by DNA
polymerases
Step 1: NTP enters & H-bonds to template DNA
Step 2: Nucleophilic attack of the 3’-OH on the α-phosphate
and pyrophosphate leaves
Step 3: Cleavage of pyrophosphate by pyrophosphatase
All Polymerases and nucleotide
modifying enzymes require Mg+2
for activity
DNA replication is extremely accurate:
but not perfect
Overall: DNA replication errors occur only
1 in every 10 billion nucleotides added (E. coli).
Polymerases accuracy: 1 error in every
50 million nucleotides added.
- Active site of polymerases is 11 Å which
restricts most non-Watson-Crick base pairs
from forming.
11 Å
Polymerase
- DNA polymerases have the ability to
proofread the sequence after the synthesis
using a bifunctional 3’-5’ exonuclease.
3’-5’
exonuclease
RNA synthesis
- Messenger RNA (mRNA)- RNA used as a
template for protein synthesis
- Ribosomal RNA’s (rRNA)- RNA constituents that
make up the ribosome
- Transfer RNA’s (tRNA)- RNA that is used as
an adapter to a specified amino acids
- Small nuclear RNA’s (snRNA)- RNA that is
used for splicing (Eukaryotes only)
RNA is synthesized by RNA polymerase
DNA-dependent RNA Polymerase differs
from DNA-dependent DNA polymerases
- Does not require a primer for synthesis
- Can unwind DNA without a helicase.
- initial unwinding requires TFIIH.
- Does not have a 3’-5’ exonuclease and thus cannot
proofread.
- The noncoding strand (antisense strand) is the strand with
the complementary RNA sequence
Genes are identified by RNA polymerase
by promoters
Promoters: conserved elements found between -70 and
+30 nucleotides from the transcription start site
Protein Synthesis (Outline)
- Genetic code vs mRNA & DNA
- Structure of Ribosome
- Activating amino acids with tRNA
- Initiation of the ribosome
- Ribosome elongation
- Ribosome termination
Crick’s Central Dogma Hypothesis (1960)
Amino acid
The Genetic Code (message in mRNA)
43 = 64 codes
First
Letter
Start
Codon
Second Letter
50S (RNA-green, proteins-blue)
Ribosome
Subunit
Proteins
RNA
30S
50S
21 types
16S
36 types
23S, 5S
65% rRNA and 35% protein
Ribosome is a ribozyme!!
tRNA
(A-site)
Picture with no tRNA
tRNA
(P-site)
tRNA
(E-site)
mRNA
30S (RNA-grey, proteins-yellow)
Amino-acyl tRNA synthetase complex
TψC arm
D arm
Anticodon
arm
Amino
acid
Evolutionary Foundations
Hierarchy in the molecular
organization
Three stages of Life’s
development
• Chemical Evolution- Simple chemicals reacted
early in life’s existence to form biological polymers
(DNA, RNA, Proteins, complex Carbohydrates).
• Biochemical Evolution- Self-organization of
biological polymers to form a living system.
• Biological Evolution- Changes within living
systems to form the complex degree of differences
in modern life forms.
Mutation & Evolution
Stanley Miller’s 1953 experiment
Small Organic &
Biological molecules
Some Organic molecules from
Stanley Miller’s Experiment
Small Organic Molecules
O
H3C
OH
H3C
N
Acetonitrile
Acetate
Small Biological Molecules
O
O
H2N
NH
HN
OH
Glycine (Gly)
O
Uracil
O
H
H
H
OH
OH
OH
OH
D-Ribose
RNA world: Why must RNA
had to exist before DNA
• RNA is less stable than DNA- More
susceptible to hydrolysis
• RNA can adopt more unique structures
• RNA can serve as a template for RNA
synthesis
• RNA can serve as an enzyme (catalyst)