A Biology Primer Part II: DNA, RNA, replication, and reproduction

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A Biology PrimerPart II DNA, RNA, replication,
and reproduction

• Vasileios Hatzivassiloglou
• University of Texas at Dallas

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Course web page

• http//www.hlt.utdallas.edu/vh/Courses/Fall09/Dat
  aTextMining.html
• Up-to-date listing of lectures, schedules,
  assignments, and supplemental course materials
• Also accessible via my home page
  http//www.hlt.utdallas.edu/vh

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Last time we covered

• Biological classification
• Organisms, tissues, cells and organelles
• Main cell functions and the role that proteins
  play
• Primary structure of proteins as a sequence of
  amino acids

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Protein manifestation

• Amino-acid sequence provides primary structure
  (one dimensional)
• Specifies proteins native state in the physical
  world
• Actual form of protein folding affected by other
  things as well a major bioinformatics problem

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Protein secondary structure

• Alpha-helix is the main secondary structure
  (local folding)
• Scale 0.5 nm wide, 1.5 nm long per amino acid
• Connection every four amino acids

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Tertiary structure and beyond
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Example protein structure
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Significance for biology

• Three-dimensional folding affects what the
  protein can do
• Predicting three-dimensional structure from amino
  acid sequence enables understanding of protein
  function
• Statistical and rule-based (including
  grammar-based models)

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Deoxyribonucleic acid (DNA)

• Another macromolecule (polymer) found in the
  nucleus of cells
• Contains all genetic information
• Consists of connected nucleotides
• Each nucleotide is connected via infrastructure
  consisting of a phosphate and a sugar molecule
  (deoxyribose)
• The structural blocks are the nucleotides or bases

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DNA Bases

• Only four bases
• Adenine (A)
• Cytocine (C)
• Guanine (G)
• Thymine (T)
• One-dimensional structure
• Chemical properties impose ordering (like
  proteins) from 5 end to 3 end

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DNA base pairing

• Hydrogen bonds between A-T and C-G (order matters)

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DNA in three dimensions

• Famous double helix
• Can be unzipped
• Anti-parallel configuration between the two
  strands (5-to-3 with 3-to-5)

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The Double Helix
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DNA size

• Measured in bases (kb or Mb)
• In bacteria, one circular helix
• In more complex organisms, organized into
  chromosomes (each one helix)
• E. coli one helix, 4.6 Mb
• Yeast 15 Mb
• Humans 23 double chromosomes, smallest has 50
  Mb, total 3 Gb

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DNA information content

• Different types of regions
• Regions that code for a protein (genes)
• Regions that regulate when the gene is expressed
  as a protein, typically nearby
• Regions that we dont know what their function is
  (junk DNA)

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Number of genes

• Varies by complexity of organism
• E. Coli about 4,000
• Yeast about 6,000
• C. Elegans (1mm worm) about 13,000
• Humans about 32,000 (thought to be 100,000)
• Genes packed and uniformly distributed in
  prokaryotes, not so in eukaryotes
• Only 3-10 of human DNA is useful

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The genome

• Total gene content for an organism
• Genes will vary from individual to individual,
  but will be substantially identical (99.9 in
  humans)

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Ribonucleic acid (RNA)

• Very similar chemically to DNA
• Differences
• the base uracil (U) replaces thymine (T). Similar
  chemically, both bond with adenine (A).
• the sugar ribose replaces deoxyribose
• generally single-stranded
• partially self-hybridizes (thus forming three
  dimensional structure)

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RNA function

• Can pack the same information as DNA
• Serves as an intermediate stage during gene
  expression
• Carries information around the cell
• Is part of certain cell structures (ribosomes)

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Major biological processes

• Replication (from DNA to DNA)
• occurs during cell division both internally and
  when the organism is reproducing
• Gene expression (from DNA to protein via RNA)
• may occur once or often

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Reproduction

• Three main mechanisms
• In single-cell organisms, one cell division
  (binary fission) is enough
• Asexual reproduction can do the same on a larger
  scale (many cells), e.g., plants that grow from
  cuttings
• Sexual reproduction is used by the majority of
  complex organisms

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Cell division

• Simpler in prokaryotic organisms (single-cell)
• A parent cell produces two identical or nearly
  identical daughter cells (exponential growth)
• Mutations can occur here (especially in bacteria)

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Phases of a cells life

• Growth (G1)
• Replication (S)
• Growth (G2)
• Division (M)
• Repeat until eventual apoptosis (cell death)

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Replication

• The DNA double helix is unzipped into two
  single complementary strands by an enzymatic
  protein (DNA polymerase)
• Each DNA strand attracts the corresponding base
  from a soup of free nucleotides
• The two strands join together (with the same
  hydrogen bonds between A-T and C-G)

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DNA replication
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Complications in replication

• Replication can only occur in the 5-to-3
  direction (can only add to the 3 end)
• One strand is replicated normally
• The other strand is replicated in short pieces
• Another protein (DNA ligase) puts the fragments
  together
• Errors can occur!

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Binary fission
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Cytokinesis

• Actual division of the cell
• Cytosol and organelles are distributed about
  equally
• Slightly different process in animals (via
  cleavage) and plants (via cell plate)

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Cleavage in animal cells

• Cleavage furrow formed by actin and myosin

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Diploid vs. haploid

• Diploid cells contain paired chromosomes from
  father and mother (homologues)
• Haploid cells have only one chromosome of each
  kind
• Organisms can be diploid (humans), haploid
  (fungi), or alternate between the two stages
  (marine algae)

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How organisms reproduce

• In asexual reproduction, a single cell division
  is enough
• In sexual reproduction, two haploid cells join
  together to form the new organism
• Haploid organisms can just join
• Diploid organisms must produce special haploid
  cells (germ cells)

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Division in diploid eukaryotes

• DNA replication (S, synthesis phase)
• Cell division (M, mitosis) for somatic cells
• Special double division (M, meiosis) division for
  germ cells or gametes