Topic 1: Introduction and overview of molecular biology and review of nucleic acids

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Topic 1 Introduction and overview of molecular
biology and review of nucleic acids

• Goals for this topic
• to understand why molecular biology is an
  important foundation for medical school
• to review the composition and structure of DNA
  and how it is packaged in our cells
• to understand the layout of our genome as a
  whole in terms of sequence variation, and
  distribution of coding and noncoding sequences

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• .just a little bit about the class
• website http//www.ag.uidaho.edu/mmbb/lfort/wwa
  mi524/home.html. This site has copies of the
  powerpoint slides (with notes appended), sample
  exam questions by topic, primers on the subjects
  with a bit more detail (if desired).
• We will cover 10 topics in 5 weeks. Each one
  will take between 1-3 h. The first 5 topics
  should essentially be review for most of you (the
  genome, replication, transcription,
  translation,lab/diagnostic techniques). The last
  5 topics are more advanced (gene control,
• epigenetics, cell cycle regulation, DNA repair,
  gene therapy) and will rely upon your
  understanding of the first five.
• SEE THE FOREST!!!! Dont get bogged down in the
  details.its the CONCEPTS you want to take home!
• Clinical examples/relevance - we will talk about
  at least one or two for each topic.
• Prokaryotic vs. eukaryotic processes - sometimes
  we will cover both to show the differences that
  can be exploited to win the upper hand against
  the bugs.

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What IS molecular biology??

• The study of the three main building blocks of
  our cells -
• DNA, RNA and proteins
• how are they produced?
• how is their production controlled?
• how do these systems go awry to cause disease?

Why should YOU study basic mo bio as med
students??

• Molecular biology and biochemistry are
  FOUNDATIONS
• Problems with the gene or gene product are often
  the underlying
• cause for the disease youre treating!

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• How does molecular biology intersect with
  medicine?
• Nucleic acid diagnostic tests
• Study of genes, genetic diseases, the human
  genome project and genetic counseling
• Molecular animal models of disease states
• Gene therapy
• Recombinant human protein production
• Cancer biology
• Infections and antibiotic development

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Molecular Biology Basics

• For DNA and RNA, the building blocks are nucleic
  acids,
• whereas for proteins, they are amino acids
• The genome is the DNA content of the organism,
  whereas the
• proteome is the collection of EXPRESSED proteins
• The DNA content of humans is 6.4 x 109 bp
  (diploid nuclear)
• 1.6 x 104 bp (mito DNA)
• This covers 30,000 genes
• The DNA spans 22 pairs of somatic and 2 sex
  chromosomes

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The Bases of DNA and RNA
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Sugars of Nucleic Acids
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Nucleosides
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Nucleotides
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DNA/RNA names to remember
Nucleoside and
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Purine Nucleotide Synthesis
PRPP (precursor ribose sugar ring- base synth.
on top)

• Basic process take ribose ring and synthesize
• a purine precursor on top of it.
• Nucleotides are synthesized as MONO-
• phosphates. KINASES convert them.
• ANTI-BACTERIAL and ANTI-CANCER
• drugs can affect this pathway.

DHF
THF
Folic Acid (we dont make)
PABA (we dont make)
SULFONAMIDES (sulfa drugs) Antibacterial drugs
that are PABA analogs. They block bacterial
synthesis of purines. METHOTREXATE Anticancer
drug that is a folic acid analog. We take up F.A.
in our diets, so an analog will block purine
biosynthesis. VERY toxic to rapidly dividing
cells!
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PURINE SALVAGE PATHWAY Recycling of purine bases
by phosphoribosyl transferases
Base PRPP BaseMP PPi

• Two PRTs for purines
• Adenine (APRT)
• Hypoxanthine, guanine (HPRT)

Lack of HPRT leads to Lesch-Nyhan Syndrome
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Lesch-Nyhan Syndrome

• X-linked point mutation
• High uric acid gout
• Mental retardation
• Cerebral palsy
• Self mutilation

Single nucleotide change in HPRT gene
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Degradation of Purine Nucleotides to Uric Acid

• Adenosine Deaminase
• Deficiency (ADA) ideal
• gene therapy target.
• normally, adenosine is
• converted to inosine
• If blocked, will go back
• up the tree to
• AMP

Synthesis
dAMP
dATP
Degradation

• This is via the action of
• ribonucleotide reductase
• If dATP pool too big, will
• block r.r. activity, which
• decreases all other pools of
• deoxynucleotides.

Gout caused by EXCESS uric acid buildup. Get
crystallization and deposition into joints.
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• The symptoms of gout
• crystallization of uric acid
• deposition of crystals in joints
• inflammation in those joints

Treatment allopurinol
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Polynucleotide
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Chain terminators as antivirals
thymine
guanine
H
Treatment for HIV
Treatment for HSV
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The Base Pairs of DNA
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Models of DNA Structure
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Model of Chromatin Packing
telomere
centromere
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Nucleosomes

• Chromatin DNA Nucleosomal proteins
• Nucleosomal core 2 each of histones H2A, H2B,
  H3 and H4
• Nucleosomal core is POSITIVELY charged
• Each core is wrapped with two superhelical turns
  of DNA
• Histone proteins can be modified by methylation,
  acetylation and phosphorylation
• Nucleosomes add a 5 fold compaction factor

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The solenoid
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Repetitive DNA elements in our genome

• Our haploid genome (one copy) 3.2x109 bp
• 1.5 of our genome (30,000 genes) is in single
  copy genes and is CODING sequence
• We are 99.9 identical to each other (and 99.8
  to chimps!) at the sequence level!
• SO WHATS THE REST????
• 60 of our genome is REPETITIVE DNA
• Some of it has structural or replication
  functions (telomeric and centromeric repeats),
  but other regions are considered functionless
• There are regions of moderate repeat (rRNAs, 5S
  rRNA, tRNAs, histones, housekeeping genes)
• There are regions of very high repeat (satellite
  regions, variable number of tandem repeat regions
  (VNTRs), Alu repeats, LINES and SINES)

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Topic 1 Introduction and overview of molecular
biology and review of nucleic acids

• Goals for this topic
• to understand why molecular biology is an
  important foundation for medical school
• to review the composition and structure of DNA
  and how it is packaged in our cells
• to understand the layout of our genome as a
  whole in terms of sequence variation, and
  distribution of coding and noncoding sequences