Chapter 12: DNA

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Chapter 12 DNA RNA

• What do you already know about DNA?

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12.1 Contributors to the Genetic Code

• Griffith and Transformation
• Worked with bacteria causing pneumonia
• Two Strains
• S strain (smooth) DEADLY
• R strain (rough) - HARMLESS

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12.1. Contributors to the Genetic Code

• Griffith Experiment
• The Experiment
• Mouse R Life
• Mouse S Death
• Mouse heat-killed S Life
• Mouse heat-killed S and R Death

Transformation changing one strain of bacteria
into another using genes. Pointed to some type
of transforming factor.
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12.1. Contributors to the Genetic Code

• Griffith
• Conclusion something transformed the living
  R-strain (harmless) into the S-strain (deadly)
  Transformation
• Oswald Avery repeated Griffiths work
• Destroyed all the organic compounds in heat
  killed bacteria except DNA Result
  transformation occurred.
• Destroyed all the organic compounds and DNA
  Result transformation did not occur.
• Conclusion DNA was the transforming factor that
  caused the change in the R-strain

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12.1 Contributors to the Genetic Code

• Alfred Hershey Martha Chase
• Question Are genes made of DNA or Proteins
• What they know viruses use other organisms to
  reproduce

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12.1. Contributors to the Genetic Code

• Alfred Hershey and Martha Chase
• Experiment
• They tagged the virus DNA with blue radioactive
  phosphorous
• They tagged the protein coat with radioactive
  sulfur

Conclusion Virus only injects DNA (DNA is the
genetic material)
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Bacteriophage Images
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HIV Images NPR Story Toddler
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12.1 Three important functions of DNA

• Store genetic information stores genes
• Copy information copy genes prior to cell
  division
• Transmit the information pass genetic
  information along to next generation

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12.2 Structure of DNA

• DNA Deoxyribonucleic Acid
• A nucleotide is composed of
• Sugar (deoxyribose)
• Phosphate group
• Nitrogenous Base
• A nucleotide is the monomer of a DNA strand
  (polynucleotide)

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12.2 Structure of DNA

• Nitrogenous Bases
• Purines Adenine Guanine (two rings in
  structure)
• Pyrimidines Cytosine Thymine (one ring)

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12.2 Structure of DNA

• DNA is a double-stranded helix
• James Watson and Francis Crick
• Worked out the three-dimensional structure of
  DNA, based on work (photos taken using x-ray
  crystallography) by Rosalind Franklin

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12.2 Structure of DNA

• The structure of DNA
• Consists of two polynucleotide strands wrapped
  around each other in a double helix (twisted
  ladder)

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12.2 Structure of DNA

• Hydrogen bonds (weak) between bases
• Hold the strands together
• Each base pairs with a complementary partner
• A with T, and G with C

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12-3 DNA Replication

• When does DNA replicate?
• DNA must copy before cell division (mitosis)
• How does it replicate?
• DNA is separated by helicase (enzyme)
• Nucleotides are added according to base pairing
  rules, using DNA polymerase (enzyme).

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12-3 DNA Replication

• DNA replication is semi-conservative
• The parent strand gives rise to two daughter
  strands.
• Each daughter strand is composed of one half the
  parent (old strand) and one half new.

Parental strand
Origin of replication
Daughter strand
Bubble
Two daughter DNA molecules
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12.3 DNA Replication

• DNA replication is a complex process
• The helical DNA molecule must untwist
• Each strand of the double helix is oriented in
  the opposite direction (antiparallel)

• DNA has three prime (3) and five prime (5)
  ends. Numbers refer to the position of the
  carbon atoms on ribose sugar.

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12.3 DNA Replication

• Using the enzyme DNA polymerase
• The cell synthesizes one daughter strand as a
  continuous piece (leading strand)
• The other strand is synthesized as a series of
  short pieces (lagging strand). Short pieces are
  called Okazaki fragments

• Okazaki fragments are then connected by the
  enzyme DNA ligase

DNA Replication Video
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DNA polymerase needs to build in a 5 to 3
direction
DNA polymerase molecule
3?
5?
Daughter strandsynthesizedcontinuously
Parental DNA
5?
3?
Daughter strandsynthesizedin pieces
3?
5?
Okazaki fragments
3?
5?
5?
3?
DNA ligase
3?
5?
Overall direction of replication
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Chapter 13 Protein Synthesis
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Chapter 13 Protein Synthesis - Overview

• The DNA of the gene is transcribed into RNA
• Which is translated into protein
• The flow of genetic information from DNA to RNA
  to Protein is called the CENTRAL DOGMA

DNA
Transcription
RNA
Translation
Protein
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Chapter 13 Protein Synthesis (Overview)
Central Dogma - FLOW IS FROM DNA TO RNA TO PROTEIN
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FLOW IS FROM DNA TO RNA TO PROTEIN
Chapter 13 Protein Synthesis (Overview)

• Genes on DNA are expressed through proteins,
  which provide the molecular basis for inherited
  traits
• A particular gene, is a linear sequence of many
  nucleotides
• Specifies a polypeptide (long protein made of
  amino acids)

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Chapter 13 Protein Synthesis (Overview)
Genes - discrete units of hereditary information
comprised of a nucleotide sequence found in a DNA
molecule.
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13-1 Messenger (mRNA)

• Monomer nucleotide
• Parts of a mRNA Nucleotide
• Ribose Sugar
• Phosphate
• Nitrogenous Base
• Three main differences between mRNA and DNA
• Ribose instead of deoxyribose
• mRNA is generally single stranded
• mRNA has uracil in place of thymine (U instead of
  T)

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13.1 RNA

• Three Types of RNA
• Messenger RNA (mRNA) carries copies of genes
  (DNA) to the rest of the cell.
• Ribosomal RNA (rRNA) make up the ribosomes.
• Transfer RNA (tRNA) transfers the amino acids
  to the ribosomes as specified by the mRNA

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• 13.1 TRANSCRIPTION The process of making mRNA
  from DNA
• Why do you need this process?
• Location of DNA? Nucleus
• Location of Ribosome? Cytoplasm
• mRNA takes code from DNA in the nucleus to the
  cytoplasm

Strand to be transcribed
DNA
Transcription
G
U
U
U
A
G
A
U
A
A
G
U
RNA
Startcondon
Stopcondon
Translation
Met
Lys
Phe
Polypeptide
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• 13.1 Transcription produces genetic messages in
  the form of mRNA
• A close-up view of transcription

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• 13.1 In the nucleus, the DNA helix unzips
• And RNA nucleotides line up along one strand of
  the DNA, following the base pairing rules
• As the single-stranded messenger RNA (mRNA) peels
  away from the gene
• The DNA strands rejoin

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RNA polymerase
DNA of gene

• Transcription of a gene
• Initiation
• Elongation
• Termination

Promoter DNA
Terminator DNA
1 Initiation
Area shown In Figure 10.9A
2 Elongation
Growing RNA
3 Termination
Completed RNA
RNA polymerase
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• 13.1 Eukaryotic mRNA is processed before leaving
  the nucleus
• Noncoding segments called introns are spliced out
  leaving only the coding exons
• A 5 cap and a poly A tail are added to the ends
  of mRNA
• Cap and tail protect mRNA

5
3
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C
C
A
A
T
T
A
U
T
C
G
T
U
G
A
C
A
U
C
C
A
C
C
A
G
A
T
T
G
G
A
T
Direction of transcription
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13.2 Translation
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13-2 Protein Synthesis - Translation

• Translation is defined as going from mRNA to
  protein
• tRNA which have amino acids attached are going to
  the ribosome.
• What are amino acids? monomers of proteins
• Does the order of amino acids matter? Yes, they
  must be in order for the protein to fold
  correctly.
• How does the correct tRNA (with amino acid
  attached) bind to the mRNA? The tRNA contains an
  anticodon which matches up with the mRNA sequence
  (codon).

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• Transfer RNA (tRNA) molecules serve as
  interpreters during translation
• Translation
• Takes place in the cytoplasm

• A ribosome attaches to the mRNA and translates
  its message into a specific polypeptide aided by
  transfer RNAs (tRNAs)
• tRNAs can be represented in several ways

Amino acid attachment site
0
Amino acid attachment site
Hydrogen bond
RNA polynucleotide chain
Anticodon
Anticodon
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13.2 Translation

• Each tRNA molecule
• Is a folded molecule bearing a base triplet
  called an anticodon on one end
• A specific amino acid
• Is attached to the other end

Amino acid attachment site
Anticodon
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13.2 Translation

• Ribosomes build polypeptides (proteins)
• A ribosome consists of two subunits
• Each made up of proteins and a kind of RNA called
  ribosomal RNA
• Translation at Ribosome

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13.2 Translation

• The subunits of a ribosome
• Hold the tRNA and mRNA close together during
  translation

tRNA-binding sites
Largesubunit
Next amino acid to be added to polypeptide
Growing polypeptide
tRNA
mRNA-binding site
mRNA
Smallsubunit
Codons
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• An initiation codon marks the start of an mRNA
  message
• mRNA, a specific tRNA, and the ribosome subunits
  assemble during initiation

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• Elongation adds amino acids to the polypeptide
  chain until a stop codon terminates translation
• Once initiation is complete amino acids are added
  one by one to the first amino acid
• The mRNA moves a codon at a time
• A tRNA with a complementary anticodon pairs with
  each codon, adding its amino acid to the peptide
  chain

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• Each addition of an amino acid
• Occurs in a three-step elongation process

Aminoacid
Polypeptide
P site
A site
Anticodon
mRNA
Codons
mRNAmovement
Stopcodon
New Peptidebond
Figure 10.14
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Figure out the exact sequence of amino acids
needed

• Take the DNA and transcribe it into mRNA
• Example TAC ATA CTA GCG ACT
• mRNA
• Take the mRNA sequence and decode it using the
  codon chart.

AUG
UAU
GAU
CGC
UGA
AUG MET
UAU TYR
GAU ASP
CGC ARG
Animation
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13.3 Mutations

• Mutations heritable changes in genetic
  information (changes to the DNA sequence)
• Two types - gene and chromosomal mutations
• Mutations can be caused by chemical or physical
  agents (mutagens)
• Chemical pesticides, tobacco smoke,
  environmental pollutants
• Physical X-rays and ultraviolet light

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13.3 Mutations

• Gene mutations
• Point Mutation mutations that affect a single
  nucleotide
• Frameshift mutation shift the reading frame of
  the genetic message.
• Can change the entire protein so it doesnt work
• Gene Mutations Explained

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13.3 Mutations
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13.3 Chromosomal Mutations

• Chromosomal mutation mutation that changes the
  number or structure of chromosomes.

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13.3 Chromosomal Mutations

• Types of chromosomal mutations
• Deletion The loss of all or part of a
  chromosome
• Duplication A segment is repeated
• Inversion part of the chromosome is reverse
  from its usual direction.
• Translocation one chromosome breaks off an
  attaches to another chromosome.

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DNA Modeling

• Each person, Construct the DNA Strand Below
• Then, construct the complimentary strand to make
  a complete DNA molecule
• Ignore the color scheme below. Use
• Cytosine Blue Deoxyribose Sugar Black
  Pentagon
• Thymine Green Phosphate White Tubes
• Adenine Orange Ribose Sugar Purple Pentagon
• Guanine Yellow tRNA Purple Plastic
• Uracil Purple Amino Acid Black Plastic
• When you have constructed the complementary
  strand join the two strands together
• with Hydrogen bonds

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Transcription and Translation Modeling

• Each group will construct an mRNA strand from the
  DNA strand below
• Then, take your mRNA strand outside the nucleus
  to the ribosome
• Use the codons of mRNA and anticodons of tRNA to
  manufacture proteins
• Use the following model pieces
• Cytosine Blue Deoxyribose Sugar Black
  Pentagon
• Thymine Green Phosphate White Tubes
• Adenine Orange Ribose Sugar Purple Pentagon
• Guanine Yellow tRNA Purple Plastic
• Uracil Purple Amino Acid Black Plastic
• Peptide Bonds (between AAs) Grey Tubes
• When you have constructed the complementary
  strand join the two strands together
• with Hydrogen bonds

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Making a DNA Molecule

• Must Contain
• Deoxyribose Sugar Pentagon shape
• Phosphate Group Circle
• At least 6 base pairs (complimentary base pair
  must be interlocking)
• Label all parts of the DNA
• Question How could the structure of a DNA
  molecule allow it to carry information and
  replicate (make copies of itself).

Backbone
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DNA Structure Questions

• What pair of scientists are largely credited for
  discovering the shape of the DNA molecule?
• Name the scientist whose photographs helped solve
  the mystery of DNAs structure
• DNA is in the shape of a _______ _______.
• What are the sides of the DNA molecule made of?
  (2 things)
• What are the rungs of the ladder made of?
• What is the monomer of DNA?
• What holds nitrogenous bases together?

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DNA early scientists

• Scientist/Experiments
• What did Griffith call the phenomenon he observed
  in the mouse experiment?
• What did Hershey and Chase mark the bacteriophage
  with? What parts were marked?
• How did marking the bacteriophage assist in
  determining DNA was the transforming factor?

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Bryson Reading Discovery of DNA

• Section 1.
• Why is it surprising that the scientists working
  in England even discovered the structure of DNA?
• When did Watson start college and when did he get
  his Ph.D.?
• Section 2.
• Why was understanding the shape of DNA so
  important?
• What did Watson remark about that is surprising
  in his autobiography?

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Bryson Reading Discovery of DNA

• Section 3.
• How did Watson depict Rosie Franklin in his book
  The Double Helix?
• What did Rosie Franklin have that at the time was
  the best in the field?
• What method was Franklin using to capture DNA
• Section 4.
• How were women treated at Kings College?
• What did Franklin do to throw her colleagues off
  the trail?
• How did Watson and Crick eventually see
  Franklins photos?

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Central Dogma Questions

• The flow of genetic information is from ______ to
  ______ to ______.
• Why does DNA send a messenger out into the
  cytoplasm?
• The manufacture of mRNA from DNA is called
  _____________.
• What cellular organelle uses the DNA codes to
  manufacture proteins?
• How is DNA ultimately associated with our
  phenotype or outward appearance?

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Homework Chapter 13 Sections 13.3 and 13.4

• Section 13.3 Mutations 372-376
• Explain the difference between the three types of
  point mutations?
• How do point mutations differ from chromosomal
  mutations?
• Explain how mutations could be harmful or
  beneficial

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• Section 13.4 Gene Regulation and Expression
  377-383
• Describe how prokaryotes turn lac genes on and
  off (mention promoters, operators, lactose,
  repressor, and RNA polymersase)?
• How do eukaryotes regulate genes during
  transcription?
• What do homeotic genes like homeobox and hox
  genes have to do with development? What is the
  difference between homeobox and hox genes?

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Drawing a DNA Molecule

• Must Contain
• Deoxyribose Sugar Pentagon shape
• Phosphate Group Circle
• At least 6 base pairs (complimentary base pair
  must be interlocking)
• Label all parts of the DNA
• Question How does the structure of a DNA
  molecule allow it to carry information and
  replicate.
• Worth 20 Points

Backbone
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• Please complete the following
• The complementary DNA strand for
• GACTGAGGA
• The mRNA strand for
• GACTGAGGA
• Translate the mRNA sequence to amino acids
• CCAUUUACG
• Translate the mRNA codons to tRNA anticodons
• CCAUUUACG

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Mutations
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