Human Genetics

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Human Genetics

• The Human Genome

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Genome

• The genome of an organism is the complete set of
  genes specifying how its phenotype will develop
  (under a certain set of environmental
  conditions).
• Diploid organisms (like us) contain two genomes,
  one inherited from our mother, the other from our
  father.
• The total DNA of an organism.
• Nuclear genome refers to the total DNA in the
  nucleus, which is distinguished from organellar
  genomes of the mitochondria and chloroplast.

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Genome size variation
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Comparison of genome organization
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Eukaryotic Genomes are Variable in Size
Marbled lungfish 139,000,000,000
Salamander 50,000,000,000
Homo sapiens 3,000,000,000
Pufferfish 400,000,000
Fruit Fly 165,000,000
Arabidopsis 100,000,000
Bakers yeast 12,067,280
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Why the big differences?

• Do Marbled Lungfish differ from Pufferfish?
• Are Lilies all that much different than
  Arabidopsis?
• These differences exist because
• Genomes have duplicated (chromosome doubling)
• Individual genes have duplicated.
• DNA exists that has no coding function.

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Gene structure

• I. Gene definition
• II. Genome organization (eukaryotic)
• 1. Genes and their noncoding regulatory
  sequences
• 2. Nonfunctional DNA
• 3. Duplicated genes
• 4. Repetitive DNA
• III. Mobile DNA
• IV. Gene Regulation

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Some Terms

• A duplicate of a gene may acquire mutations and
  emerge as a new gene.
• Noncoding DNA a sequence of DNA contained in
  eukaryotic genomes that does not encode any
  genetic information and often consists of
  repetitive sequences.
• Expression DNA transcribed into RNA and RNA
  turned into protein are expressed. The
  regulation of this process is called gene
  expression.

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Nomenclature on DNA quantity

• bp one base pair within a double-stranded
  DNA
• kb 1,000 base pairs of double-stranded DNA
• mb 1 million base pairs of double-stranded
  DNA
• n number of chromosomes in a haploid genome
• 2n number of chromosomes in a diploid genome

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Definition(s) of a Gene

• 1. A hereditary unit that is composed of a
  sequence of DNA and occupies a specific position
  or locus.
• 2. Broadly, any genetic determinant of a specific
  functional gene product.
• 3. Molecular definition
• Entire nucleic acid sequence necessary for the
  synthesis of a functional polypeptide (protein
  chain) or functional RNA

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Genes and Their Products

• The majority of genes are expressed as the
  proteins they encode.
• The process occurs in two steps
• Transcription DNA -gt RNA
• Translation RNA -gt protein
• This is the Central Dogma" of Biology
• DNA makes RNA makes protein.

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The Central Dogma of Molecular Biology

• WHY?
• The DNA can retain integrity
• The RNA step allows amplification
• Multiple steps allow multiple points of control

Protein
DNA
Translation
RNA
Transcription
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Most Genes Encode Proteins

• Original Concept of the Gene
• One gene one enzyme
• This concept does not hold for those proteins
  that consist of two or more different subunits.
• Revised Concept
• One gene one messenger RNA one peptide.

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RNA Genes

• Some RNAs (tRNA, rRNA, snRNA, mtRNA) dont code
  for proteins that are translated.
• However, these are still referred to as
  genes-they are specific functional gene products.
  
• Other DNA sequences regulate the transcription of
  other genes and can act like genes in some ways.

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Genes are interspersed along DNA molecules, being
separated by DNA sequence of unknown function
(intergenic regions)
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Coding region

• Nucleotides (open reading frame) encoding the
  amino acid sequence of a protein

The molecular definition of gene includes more
than just the coding region.
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Noncoding regions

• Regulatory regions
• RNA polymerase binding site
• Transcription factor binding sites
• Introns
• Polyadenylation poly(A) sites

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Nonfunctional DNA
80 kb

• Higher eukaryotes have a lot of noncoding DNA
• Some has no known structural or regulatory
  function (no genes)

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Duplicated genes

• Encode closely related (homologous) proteins
• Clustered together in genome
• Formed by duplication of an ancestral gene
  followed by mutation

Five functional genes and two pseudogenes
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Mobile DNA

• Moves within genomes
• Most of moderately repeated DNA sequences found
  throughout higher eukaryotic genomes
• L1 LINE is 5 of human DNA (50,000 copies)
• Alu is 5 of human DNA (gt500,000 copies)
• Some encode enzymes that enable movement

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Transposition

• Movement of mobile DNA
• Involves copying of mobile DNA element and
  insertion into new site in genome

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Why?

• Molecular parasite selfish DNA
• Probably have significant effect on evolution by
  facilitating gene duplication, which provides the
  fuel for evolution, and exon shuffling

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RNA or DNA intermediate

• Transposon moves using DNA intermediate
• Retrotransposon moves using RNA intermediate

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LTR (long terminal repeat)

• Flank viral retrotransposons and retroviruses
• Contain regulatory sequences
• Transcription start site and poly(A) site

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LINES and SINES

• Nonviral retrotransposons
• RNA intermediate
• Lack LTR
• LINES (long interspersed elements)
• 6000 to 7000 base pairs
• L1 LINE (5 of human DNA)
• Encode enzymes that catalyze movement
• SINES (short interspersed elements)
• 300 base pairs
• Alu (5 of human DNA)

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Human Disease and Mobile DNA

• Movement (transposition) of LINES and SINES can
  cause mutations and genetic disease by insertion
  into essential genes
• Hemophilia (blood clotting factor VIII gene)
• Muscular dystrophy (DMD)
• Colon cancer (APC)

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RNA Transcription

• The process of releasing information contained in
  a DNA sequence, because DNA itself is used only
  for storage and transmission.
• The sequence of bases in the DNA template is
  copied into an RNA sequence, which is either used
  directly or translated into a polypeptide.

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Noncoding DNA can be Part of Transcribed Genes

• Regulatory regions (Promoters)
• Introns
• Poly A Addition sites
• 5 untranslated regions
• 3 untranslated regions.

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Basic Gene Structure
-35
-10
Prokaryotes like E. coli
CAAT
TATA
GC
Humans and other Eukaryotes
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Bacterial Gene

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Human Genes

• Most have introns
• Produce monocistronic mRNA only one encoded
  protein
• Large ( 1000-gt1,000,000 base pairs)

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Gene Transcription and Regulation
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A Puzzle about Cells

• Each Cell has a complete copy of all the DNA.
  And yet, cells are different.
• This is the theoretical basis of organism
  cloning.
• So cells are only using some of the DNA to make
  RNA to make proteins at any time.
• How does the cell know which DNA to chose to
  transcribe?
• External environment sends signals that are
  recognized, and transcription is turned on or off
  in response to the signals.

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Transcription

• Transcription is the synthesis of RNA from a DNA
  template.
• Main Types of RNA each have different roles in
  the cell
• mRNA Messenger RNA
• tRNA Transfer RNA
• rRNA Ribosomal RNA
• mtRNA Mitochondrial RNA
• snRNA Small nuclear RNA

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rRNA and tRNA are Cogs in the Machinery

• rRNA is a structural part of the ribosome
• tRNA helps the protein machinery to read the mRNA
• Neither of these types of RNAs actually carries
  any information

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Messenger RNA

• Messenger RNA carries the information in the DNA
  to the protein translation machinery (ribosomes)
• Serves as the template for protein synthesis
• Which mRNAs are transcribed in a cell decide the
  fate of that cell since they dictate which
  information in the DNA is read by the protein
  translation machinery

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RNA molecules

• Synthesized by RNA polymerases using DNA as a
  template.
• Polymer of ribonucleotides, where each consists
  of a phosphate group (PO4), ribose sugar, and a
  base (adenine, guanine, cytosine, or uracil).
• Following synthesis of an RNA strand, it remains
  single-stranded.

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Gene Regulation can occur at any of these steps

• Initiation- highly regulated step
• Elongation- the rate at which the mRNA is made
  can control how quickly its made
• Termination- premature termination can mean that
  the whole mRNA never gets made and neither does
  what it codes for
• Like receiving only part of the instructions on
  how to put together your easy to assemble
  bookcase/desk/whatever

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Steps of RNA Transcription

• Initiation
• Elongation
• Termination
• All RNA transcription is performed by enzymes
  called RNA polymerases.
• RNA transcription starts at a Promoter sequence
  (analogous to ORI for DNA replication).

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Transcription of mRNA in Humans

• Steps involved are the same as in prokaryotes
• Initiation
• Elongation
• Termination
• Mediated by RNA polymerase II
• Very complex enzyme with many subunits

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Human Transcription

• Has to be more control of how more complex
  genetic material is read to create more variety
  (multicellular)
• RNA has to be transcribed in the nucleus and then
  transported to the protein translation machinery
  in the cytoplasm before it can be read.

DNA
Nucleus
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Human genes

• Most have introns
• Produce monocistronic mRNA only one encoded
  protein
• Large genes

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Initiation

• Initiation occurs at promoters as in prokaryotes-
  eukaryotic promoters are not well-characterized
  but have some well conserved elements- including
  the TATA box and CAAT box (both have AT pairs)
• In addition to the promoters there are region in
  the DNA called enhancers to which transcription
  factors bind and regulate which DNA is read and
  encoded in mRNA

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Transcription Factor Function
Pol
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Transcription Factors

• Although transcription is performed by RNA
  Polymerase, it needs other proteins to produce
  the transcript.
• These proteins are either associated directly
  with RNA Polymerase or help it bind to the DNA
  sequences upstream of the initiation of
  translation..
• These associated proteins are called
  transcription factors.

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RNA transcription begins by the assembly of the
RNA polymerase on a promoter region.
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Orientation of promoter elements specifies the
direction of transcription
-35
-10
prokaryote
CAAT
TATA
GC
eukaryote
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Transfer of Information
Gene
mRNA
exon intron exon intron
exon
Exon - portion of the gene that contains DNA
sequences that will be translated into protein.
Intron - portion of the gene that will be cut out
before translation
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Transfer of Information
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Reading the Genes in the Genome
Signal recognizing
Transcribing
Processing
mRNA
AAA