Suggestions for success

1
Suggestions for success

• Read the book as much as you can.
• Print out the slides (1-2/page) and bring them to
  lecture.
• Take additional notes on the slides in lecture
  (or tape the lecture).
• Go to Discussion Sections to ask questions, and
  take quizzes to test your understanding and
  knowledge.
• You can also form small study groups and share
  questions.
• Dont wait until the day before the exam to cram.

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Molecular Biology - whats in a name?

• Molecular Biology was born in the middle part
  of the 19th century as a new discipline focused
  on understanding the molecular basis of the most
  fundamental of life processes those involving
  the reproduction and expression of genetic
  information.
• -study of gene structure and function at the
  molecular level.

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Molecular Biology Timeline
DNA discovered by F. Meischer
1869
1910
Genes on chromosomes T.H. Morgan
1941
One gene-one enzyme, Beadle Tatum
1944
DNA is genetic material Avery, Mcleod McCarty
1953
Structure of DNA Watson, Crick, Franklin, Wilkins
1961
Discovery of mRNA Brenner, Jacob Meseleson
1966
Finished unraveling the code Nirenberg Khorana
1972
Recombinant DNA made in vitro P. Berg
DNA cloned on a plasmid H. Boyer S. Cohen
1973
Discovery of reverse transcriptase H. Temin
1973
1977
Rapid DNA sequencing F. Sanger W. Gilbert
1977
Discovery of split genes Sharp, Roberts et al.
1982
Discovery of ribozymes T. Cech S. Altman
1986
Creation of PCR K. Mullis et al.
Human Genome Project Venter, Collins and many
others
2001
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The modern framework of Molecular Biology
Transcription
Processing
Translation
DNA preRNA RNA Protein
Replication Repair
folding assembly processing
DNA
Central Dogma
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What was the first informational macromolecule?

• Proteins ?
• DNA ?
• RNA ?
• Macromolecule no longer used in modern cells ?

RNA is the only currently used macromolecule that
is both a carrier of genetic information and an
enzyme.
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The RNA World

• The RNA world hypothesis posits that there was
  a stage early in the early evolution of life that
  was dominated by RNA.
• Moreover, the functions of RNA in modern cells
  are only remnants of its previous roles.

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Possible remnants of the RNA World

• Self-splicing introns
• Rnase P (ribozyme that cleaves tRNA precursors)
• Self-cleaving viral RNAs
• Peptidyl transferase in the ribosome
• Nucleotides (ribo) involved in
• metabolism (e.g., ATP, UTP, NADH, NADPH)
• signaling (cAMP, cGMP, GTP, ITP)
• assembly of complexes (GTP and ATP)
• Energy for motility, ion pumping, etc. (ATP, GTP)

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• Deoxyribonucleic acid (DNA)
• is the genetic material
• Stores genetic information in the form of a code
  a linear sequence of nucleotides.
• Replicated by copying the strands using each as
  a template for the production of the
  complementary strand.

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3 Ways of Depicting DNA Structure
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Nucleosides (of DNA) Precursors to Nucleotides
Nucleoside base sugar
Sugar deoxyribose 5 carbons, no OH on the 2nd
(or 2) carbon base is attached to carbon 1
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The 4 Nucleotides of DNA
12
RNA
Ribose replaces deoxyribose uracil replaces
thymine
13
e.g., AMP is a ribonucleotide, dAMP is a
deoxyribonucleotide
14
In DNA and RNA, nucleotides are held together by
phosphodiester bonds.
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Higher Order RNA Structure
Stem-loops are common elements of RNA structure.
Stems are double-stranded regions of RNA that are
A-form helices. They follow Watson-Crick base
pairing rules. (DNA is typically a B-form
helix).
Stem
loop
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Secondary structure diagram
Tertiary structure diagram
Tetrahymena rRNA intron
Cr.LSU rRNA intron
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Figure 2.16
A
B
Z
Residues/turn 11 10
12
Clockwise turn
Anti-clockwise turn
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Double-stranded (DS) DNA statistics (B-form)

• Helix is right handed
• 10 base-pairs/turn
• 3.4 nm (34 angstroms)/turn
• Helix has a major groove and a minor groove.

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What chemical forces hold the DNA strands
together? (also applies to double-stranded
regions of RNA)
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1. Hydrogen bonds between bases
Also important that the purine-pyrimidine base
pairs are of similar size.
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2. DNA strands also held together by base
stacking Van der Waals interactions between
pairs of neighboring bases
Evidence Compounds that interfere with Hydrogen
bonds (urea, formamide) dont separate strands by
themselves, still requires heat
3. Double-stranded helix structure also promoted
by having phosphates on outside, interact with
H2O and counter ions (K, Mg2, etc.)
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Study Helix Stability with Melting Curves

• DNA melting curve of Streptococcus DNA.
• When DNA melts, the 2 strands come apart, and its
  absorbance in the UV region increases.

Tm temp. at which 50 of DNA is melted.
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Re-Annealing or Hybridization

• Works with
• DNA - DNA
• DNA - RNA
• RNA - RNA

Basis of many techniques in molecular biology.
Figure 2.20
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G-C content determines melting temperature
varies among organisms

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DNA Replication in Prokaryotes and Eukaryotes

• Overall mechanism
• Roles of Polymerases other proteins
• Mitochondrial DNA replication

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Few Questions

• Is DNA replication conservative,
  semi-conservative or random dispersed? Fig. 20.1
  and 20.3.
• Is DNA replication bidirectional? Fig. 20.11.
• Does DNA replication start at the same location
  or random location?