The Structure and Function of DNA

1
The Structure and Function of DNA

• Chapter 10
• Part II

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Figure 10.10
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The Genetic Code

• Set of rules relating nucleotide sequence to
  amino acid sequence
• - redundancy of the code but no ambiguity
• In 1961 an American biochemist Marshall
  Nierenberg synthesized an artificial RNA molecule
• - linked together RNA nucleotides having uracil
  as their base
• - UUU always coded for phenylalanine

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• Translate the sequence CCAUUUACG

Figure 10.11
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Universality of the Code

• The genetic code is shared by all organisms
• - from the simplest bacteria to the most complex
  plants and animals
• - genes can be transcribed and translated after
  transfer from one species to another

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• Researchers incorporated a gene from a firefly
  into the DNA of a tobacco plant
• The gene codes for the firefly enzyme that
  produces a glow

Figure 10.12
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Transcription From DNA to RNA

• Transcription transfer of genetic information
  from DNA to RNA
• - an RNA molecule is transcribed from a DNA
  template
• As with replication the 2 DNA strands must first
  separate
• - but only one strand serves as a template
• - RNA nucleotides take their places one at a
  time along the DNA template strand by forming
  hydrogen bonds
• - the RNA nucleotides are linked by the
  transcription enzyme RNA polymerase

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Fig 10.13a

• RNA nucleotides base-pair one by one with DNA
  bases on the DNA template strand
• The enzyme RNA polymerase links the RNA
  nucleotides into an RNA chain

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Transcription of an Entire Gene

• Special DNA nucleotide sequences inform the RNA
  polymerase
• - where to start where to stop the
  transcribing process
• Initiation of Transcription the first phase,
  transcription starts
• - the start transcribing signal, is a
  nucleotide sequence called a promoter
• - RNA polymerase attaches to the promoter
• - RNA synthesis begins
• - for any gene the promotor dictates which of
  the 2 strands is to be transcribed

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• RNA Elongation the second phase of
  transcription, the RNA strand grows longer
• - as RNA synthesis continues, the RNA strand
  separates from its DNA template
• - allows the separated DNA strands to recombine
• Termination of Transcription the third phase,
  termination, transcription stops
• - special sequence of bases in the DNA template,
  the terminator, signals the end of the gene
• - at this point, the RNA polymerase detaches
  from the RNA molecule and the gene

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Figure 10.13a,b
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The Processing of Eukaryotic DNA

• Prokaryotic cells lack nuclei RNA transcribed
  from a gene functions immediately
• - the messenger molecule, mRNA is translated
  into protein
• Eukaryotic cells have nuclei localizes
  transcription in the nucleus
• - also modifies, or processes, the RNA
  transcripts before the mRNA moves to the
  cytoplasm for translation

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RNA Processing

• Addition of a cap and tail extra nucleotides
  added to the ends of the RNA transcript
• - protects the RNA from attack by cellular
  enzymes
• - help ribosomes recognize the RNA as mRNA
• Removing introns noncoding stretches of
  nucleotides are removed
• - introns are interspersed between the
  nucleotides that code for amino acids
• - the coding regions, or exons, are parts of the
  gene that are expressed

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• RNA splicing occurs before the RNA leaves the
  nucleus
• - introns are removed, and the exons are joined
  to produce an mRNA molecule
• RNA splicing plays a significant role in humans
• - allows approximately 25,000 genes to produce
  many 1000s more polypeptides
• - this is accomplished by varying the exons that
  are included in the final mRNA

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Figure 10.14
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Translation The Players

• Is the conversion from the nucleic acid language
  to the protein language
• First important player is the mRNA produced by
  transcription
• - the machinery used to translate mRNA requires
  enzymes and energy, such as _____
• - also requires 2 important players ribosomes
  and another kind of RNA called transfer RNA (tRNA)

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Transfer RNA (tRNA)

• Acts as a molecular interpreter
• - translates the 3-letter word (codon) of
  nucleic acids to a one-letter word (amino acid)
  of proteins
• - tRNA matches amino acids with codons in mRNA
  using anticodons
• To accomplish translation, tRNA molecules must
  carry out 2 distinct functions
• 1) pick up the appropriate amino acids from the
  cytoplasm
• 2) recognize the appropriate codons in the mRNA

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• A tRNA molecule is made of a single strand of RNA
  polynucleotide chain of 80 nucleotides
• - chain twists and folds forming several
  double-stranded regions where short stretches of
  RNA base-pair
• - one end of the folded molecule is a special
  triplet of bases, anticodon
• - anticodon triplet is complementary to a codon
  triplet on the mRNA
• - during translation, the anticodon on the tRNA
  molecule recognizes its codon on the mRNA
  (base-pairing rules)
• - at the other end of the tRNA molecule is a
  site where an amino acid can attach

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Structure of a tRNA Polynucleotide

• A twisted rope appendages are the nitrogenous
  bases
• 3-nucleotide segment at one end (purple) - site
  where an amino acid will attach
• 3-base anticodon at the bottom of the molecule
  will base-pair with its codon

Figure 10.15
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Ribosomes

• Organelles that coordinate the function of making
  a polypeptide consist of 2 subunits
• - each subunit is made up of proteins and
  ribosomal RNA (rRNA)
• - an assembled ribososme has a binding site for
  mRNA on its small subunit and
• - 2 binding sites for tRNA on its large subunit,
  the
• - P site, holds the tRNA carrying the growing
  polypeptide chain, the
• - A site, holds a tRNA carrying the next amino
  acid to be added to the chain

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Figure 10.16a
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• A ribosome holds one molecule of mRNA, 2
  molecules of tRNA
• Subunits act like a vise, holding the tRNA and
  mRNA molecules close together
• The ribosome can then connect the amino acid from
  the A site tRNA to the growing polypeptide

Figure 10.16b
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Translation The Process

• Translation can be divided into the same 3 phases
  as transcription
• - Initiation
• - Elongation
• - Termination

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Initiation

• The first phase brings together
• - The mRNA
• - The first amino acid with its attached tRNA
• - The two subunits of the ribosome
• Nucleotide sequences at either end of the mRNA
  are not part of the message
• - but, along with the cap and tail help the mRNA
  bind to the ribosome
• - determines where translation will begin so
• - the mRNA codons will be translated into the
  correct sequence of amino acids

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A Molecule of mRNA
Figure 10.17

• Pink ends are nucleotides that are not part of
  the message
• Along with the cap and tail help the mRNA attach
  to the ribosome but are not translated
• Initiation of translation occurs in 2 steps

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Figure 10.18

• 1. mRNA binds to the small
• subunit a special initiator tRNA
• binds to the start codon, the
• initiator tRNA carries Met its
• anticodon UAC binds to the start
• codon, AUG

• 2. The large ribosomal subunit
• binds to the small one, creating a
• functional ribosome the initiator
• tRNA fits into the P site on the
• ribosome

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Elongation

• Once initiation is complete, amino acids are
  added one by one to the first amino acid
• Each addition occurs in a 3-step elongation
  process
• Step 1 Codon recognition
• Step 2 Peptide bond formation
• Step 3 Translocation

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• Step 1, codon recognition the anticodon of an
  incoming tRNA carrying its amino acid, pairs with
  the mRNA codon in the A site of the ribosome
• Step 2, peptide bond formation the polypeptide
  leaves the tRNA in the P site and
• - attaches to the amino acid on the tRNA in the
  A site
• - the ribosome catalyzes bond formation now the
  chain has one more amino acid
• Step 3, translocation the P site tRNA now
  leaves the ribosome, and
• - the ribosome moves the remaining tRNA,
  carrying the growing polypeptide to the P site
• - the mRNA and tRNA move as a unit which brings
  into the A site the next mRNA codon

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Figure 10.19
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Termination

• Elongation continues until a stop codon reaches
  the ribosomes A site
• - stop codons UAA, UAG, UGA
• Completed polypeptide, typically several 100
  amino acids long, is released, and the ribosome
  splits into its subunits

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Review DNA?RNA?Protein

• Is the flow of genetic information in the cell
• In eukaryotic cells, transcription the stage
  from DNA to RNA, occurs in the nucleus, and
• - the mRNA is processed before it enters the
  cytoplasm
• Translation is rapid a single ribosome can make
  an average-sized polypeptide in less than a
  minute
• - as it is made a polypeptide coils and folds,
  assuming a 3-dimensional or tertiary shape
• - several polypeptides may come together,
  forming a protein with a quaternary structure

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Figure 10.20
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Transcription and Translation

• Are the processes whereby genes control the
  structures and activites of cells, or
• - the way the genotype produces the phenotype
• Originates with the information in a gene
• - a specific linear sequence of nucleotides in
  DNA
• - the gene serves as a template for the
  transcription of a complementary sequence of
  nucleotides in mRNA
• - mRNA specifies the linear sequence in which
  amino acids appear in a polypeptide, and
• - the proteins that form determine the
  appearance and capabilities of the cell and
  organism

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Mutations

• A mutation is any change in the nucleotide
  sequence of DNA
• - occasionally a base substitution leads to an
  improved protein or
• - one with new capabilities that enhance the
  success of the mutant organism and its
  descendants
• - more often, mutations are harmful

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Fig 10.21

• The molecular basis of sickle-cell disease the
  sickle-cell allele
• differs by only one nucleotide. The difference
  changes the
• mRNA codon from one that codes for glutamate
  (Glu) to one
• that codes for valine (Val)

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Types of Mutations

• Within a gene can be divided into 2 general
  categories base substitutions and base
  insertions or deletions
• Base substitution replacement of one base, or
  nucleotide, by another can result in
• - no change in the protein, redundancy of the
  genetic code
• - a change in the amino acid coding (missense
  and nonsense mutations) which might be crucial to
  the life of the organism

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Missense Mutations
Figure 10.22a
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• Insertions and deletions often have disastrous
  effects
• - mRNA is read as a series of nucleotide
  triplets during translation, adding or
  subtracting nucleotides may alter the reading
  frame
• - all the nucleotides downstream will be
  regrouped into different codons
• - the altered polypeptide is likely to be
  nonfunctional

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Figure 10.22b
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Mutagens

• Mutagenesis, the creation of mutations, can occur
  in a number of ways
• - errors during DNA replication or recombination
  are called spontaneous mutations (de novo)
• - physical or chemical agents called mutagens
• - most common physical mutagen is high-energy
  radiation, such as X-rays and UV light)
• - chemical mutagens are of various types, one
  type consists of chemicals that are similar to
  normal DNA bases

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• Many mutagens can act as carcinogens cancer
  causing agents
• - UV light and smoking lifestyle practices can
  help
• Although mutations are often harmful they can
  be useful both in nature and in the lab
• - they are the source of the rich diversity of
  genes in the living world
• - they contribute to the process of evolution by
  natural selection

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Fig 10.23

• Mutations are the ultimate source of diversity of
  life

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Viruses Genes in Packages

• Viruses sit on the fence between life and nonlife
• - they exhibit some, but not all characteristics
  of living organisms
• - viruses have genes and a highly organized
  structure
• - but are not able to reproduce on their own
• - a virus can survive only by infecting a living
  cell with genetic material that directs the host
  cells molecular machinery to make more viruses

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Fig 10.24

• Adenovirus infects the human respiratory
  system, consists
• of DNA enclosed in a protein shell. At each
  vertex of the
• polyhedron is a protein spike, helps the virus
  attach to a cell

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Bacteriophages

• Or phages attack bacteria
• Once they infect a bacterium, most phages enter a
  reproductive cycle, the lytic cycle
• - after many copies of the phage are produced
  the bacterium lyses (breaks open)
• - some also reproduce by the lysogenic cycle
  viral DNA replication occurs without phage
  production or the death of the cell

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Fig 10.25

• The phage consists of a molecule of DNA enclosed
  within a
• protein structure tail fibers bend when they
  touch the cell
• surface the tail is a hollow rod enclosed in a
  springlike
• sheath, as the fibers bend, the spring
  compresses, the
• bottom of the rod punctures the membrane

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Figure 10.26
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Plant Viruses

• Can stunt growth and diminish crop yields most
  have RNA rather than DNA
• - many, like the tobacco mosaic virus are
  rod-shaped with a sprial arrangement of proteins
  surrounding the nucleic acid
• - a virus must get past the plants outer
  protective layer of cells and so a weak plant is
  more susceptible to infection
• - infected plants may pass viruses to their
  offspring
• - there is no cure for most viral plant diseases
• Genetic engineering methods have been used to
  create virus-resistant plants

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Fig 10.27

• Tobacco mosaic virus the rod-shaped virus has
  RNA as
• its genetic material

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Animal Viruses

• Viruses that infect animals are common causes of
  disease

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Figure 10.28
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Figure 10.29
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Figure 10.30a
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Figure 10.30b
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Figure 10.30c
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Figure 10.31
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Figure 10.32
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Figure 10.33