Welcome to My Molecular Biology Class

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Welcome to My Molecular Biology Class
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Molecular Biology of the Gene, 5/E --- Watson et
al. (2004)
Part I Chemistry and Genetics Part II
Maintenance of the Genome Part III Expression
of the Genome Part IV Regulation Part V Methods
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Chemistry and Genetics
Ch 1 The Mendelian View of the World Ch 2
Nucleic Acids convey genetic information Ch 3
The importance of weak chemical interactions Ch
4 The importance of high-energy bonds Ch 5 Weak
and strong bonds determine macromolecular
structure
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Chapter 3 The importance of weak chemical
interactions
Weak bonds indeed are vital for life, partly
because they can form and break under the
physiological conditions present with cells.
(Dynamics is important)
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Pages 45-53 are important to read
List the reasons making weak bond vital for life
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Chapter 5 Weak and strong bonds determine
macromolecular structure
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Ch 5 Weak and strong bonds determine
macromolecular structure

• Higher-order structures are determined by intra-
  and intermolecular interactions
• The specific conformation of a protein results
  from its pattern of hydrogen bonds
• Most proteins are modular, containing two or
  three domains
• Weak bonds correctly position proteins along DNA
  and RNA molecules
• Allostery Regulation of a proteins function by
  changing its shape

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Why Watson et al. want to tell us some stories
about genetics and chemistry before we start the
molecular biology?
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Genetics ?? Inheritable traits
(Mendel) Genetic material-DNA (Avery) Central
Dogma ???? (Watson and Crick)

• Chemistry-mechanisms ??
• Weak chemical bond? interactions
• Strong chemical bond ?energy transfer
• 3.Weak and strong bonds determine macromolecule
  structure

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The focus of Ch1 and Ch2 Recognizing scientists
and science ????????
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1. Recognizing the life of scientists (????????).
2. Recognizing the value and nature of science
   (??????????).
3. Recognizing the noble characters displayed by
   scientists (??????????) love of the beauty of
   nature (?????????), the faith of your own
   creativity (??????????) and the hope to be
   recognized (??????????????-communication is
   important).

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Chapter 1 The Mendelian View of the World
(??????????)
To explain how the genetic traits (????) are
transferred from the parents to the offsprings.
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Two important lessons to learn from Mendels
discovery
Recognizing the life of a scientist Box 1-1

1. The attitude to science interested in
   discovering the wonders of the nature (laws,
   mechanisms)
2. The principle to conduct science using simple
   models to understand the complicate or unknown
   story

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Recognizing the beauty of science Mendels
discovery
The principle of independent segregation
(??????) (Mendels first law)
---The trait appearing in F1 progeny is called
dominant the one not appearing is called
recessive. ---The various traits are controlled
by pairs of factors (which we now call genes)
Figure 1-1 How Mendels first law explains the
31 ratio of dominant to recessive phenotypes
among the F2 progeny.
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Recognizing the beauty of science Mendels
discovery
Some alleles are neither dominant or recessive
(And some phenotypes are determined by more than
one gene) (The luck of Mendels discovery a
simple trait)
Figure 1-2 The inheritance of flower color in
the snapdragon (???).
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Recognizing the beauty of science Mendels
discovery
Principle of independent assortment (??????)
(Mendels second law)
---When more than one characteristic are
examined, the progenies showing recombined
traits appear.
Figure 1-3 How Mendels second operate.
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Discussion 1

• Why Mendelianism and Darwinism conflicted
  initially, how the conflict was resolved? (P15-16)

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Discussion 2 Scientist and Science
A hypothesis/theory that is too broad to be
specify or to be tested in the strict concept of
science too complicate and can be revised
forever if you do not want to give it up.
A testable hypothesis/theory Simple and beautiful
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Chapter 2 Nucleic Acids convey genetic
information
The stories/efforts led to the fundamental
knowledge of life, which open a new era of modern
biology.
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Ch 2 Nucleic Acids convey genetic information
Averys Bombshell (1944) DNA can carry genetic
specificity
The Double Helix (1953)
The genetic information within DNA is conveyed by
the sequence of its four nucleotide building
blocks
The Central Dogma (1956)
Establishing the direction of protein synthesis
The Era of Genomics (2000)
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The background of the discovery
Breakthrough in the thinking darkness

• By the 1930s, geneticists began speculating as to
  what sort of molecules could have the kind of
  stability that the gene demanded, yet be capable
  of permanent, sudden change to the mutant forms
  that must provide the basis of evolution...
• It was generally assumed that genes would be
  composed of amino acids because, at that time,
  they appeared to be the only biomolecules with
  sufficient complexity to convey genetic
  information.
• This hypothesis is eventually dead from its
  shaking base and attractive complexity.

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Averys Bombshell (1944) DNA can carry genetic
specificity
A story written for 16 years
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1928 by Frederick Griffith
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1944 by Osward T. Avery
The transforming activity was destroyed by
deoxyribonuclease (available at the time), but
not by ribonuclease nor various proteolytic
enzymes
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Thinking 1 what do you learn from the efforts of
George W. Beadle and Edward Tatum (1940s),
Frederick Griffith (1928), Osward T. Avery
(1940s)
Thinking 2 Why Avery made more recognizable
contribution to the field than did Griffith?
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The Double Helix (1953)
The foundation of molecular biology
Francis H. Crick James D. Watson
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Thinking 3 what led to the success of Watson and
Crick?
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• Crick is best known for his work in
  the discovery of the double helix, but since then
  he has made many other discoveries. After his
  discovery of the double helix, Crick went to work
  on finding the relationship between DNA and
  genetic coding. During this study with Vernon
  Ingram, they discovered the function of the
  genetic material in determining the specificity
  of proteins. In 1957, Crick began work with
  Sydney Brenner to determine how the sequence of
  DNA bases would specify the amino acid sequence
  in proteins.
• Crick "established not only the basic
  genetic code, but predicted the mechanism for
  protein synthesis" (McMurray, 427) This worked
  led to many RNA/DNA discoveries and helped in the
  creation of the DNA/RNA dictionary. In 1960 Crick
  began to study the structure and possible
  functions of certain proteins associated with
  chromosomes called histones. Crick finally left
  Cambridge Laboratories in 1976 to become
  Kieckhefer Professor at Salk Institute for
  Biological Studies in San Diego, California. It
  was there that Crick began his present project of
  the study of the brain.

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Rosalind Elsie Franklin Pioneer Molecular
Biologist From www.sdsc.edu/ScienceWomen/franklin.
html (San Diego Supercomputer Center)
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The Central Dogma (1953-1956)
Setting the platform for molecular biology only
takes 0.5 year or 3.5 years Exciting days of
biologists
Transcription
RNA
Protein
DNA
Translation
Replication
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Gene Expression
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The revised central dogma ---The framework of
this course
??????
??????
RNA processing
Gene regulation
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Ch 2 Nucleic Acids convey genetic information
The purpose of Molecular Biology of the genes is
to provide a firm foundation for understanding
how DNA functions as the template for biological
complexity.
Remember this book is living in the age of the
Central Dogma in understanding life, post-genomic
era will certainly tell us a more complex but I
hope a clear story of life.
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Part 2, Maintenance of the Genome, describes the
structure of the genetic material and its
faithful duplication. Part 3, Expression of the
Genome, shows how the genetic instructions
contained in DNA is converted into proteins Part
4, Regulation, describes strategies for
differential gene activity that are used to
generate complexity within the organisms and
diversity among organisms
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Part 5, Methods, describes various laboratory
techniques, bioinformatics approaches, and model
systems that are commonly used to investigate
biological problem.