Making Proteins

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Making Proteins
Making Proteins
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DNA Timleline

• 1843 Mendel Traits are inherited in specific
  ratios by genes
• 1905 Morgan genes are on chromosomes
• Chromosomes are DNA and proteins, which is the
  hereditary material?
• 1928 Griffith transformation a change in the
  genotype and phenotype due to assimilation of
  external DNA
• 1944 Avery, McCarty and MacLeod said
  transformation due to DNA
• 1952 Hershey and Chase bacteriophage or phage (a
  virus that infects bacteria) injects its DNA
  into bacteria
• 1947 Chargaff Amount of DNA differs in all
  organisms but A and T in 30 ratios and G and C
  in 20 ratios (A pairs with T and C pairs with
  G).
• 1950s What does DNA look like?

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Watson and crick

• While visiting Cambridge University Maurice
  Wilkins was showing Watson the laboratory and
  Watson saw Rosalind Franklins X-ray photograph of
  DNA
• The picture helped Watson and Crick discover the
  3-D structure and Semi-conservative Double Helix
  nature of DNA
• (figure 16.5, 16.6, 16.8)

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http//www.vcbio.science.ru.nl/images/cellcycle/mc
ell-transcription-translation_eng_zoom.gif
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Making Proteins

• DNA Replication
• Transcription
• Translation

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Parts of DNA

• DNA As the Genetic Material
• DNA is a double helix like twisted ladder with
  rigid rungs
• The side or backbone is made of sugar-phosphate
  components
• The rungs are pairs of nitrogen bases

http//www.ac-rennes.fr/pedagogie/svt/cartelec/car
telec_lyc/premiere_s/vegetal/adn/adn_frag.gif
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Replication DNA - DNA

• The replication of DNA begin at the origins of
  replication
• Helicase proteins bind to the origin of
  replication and separate the two strands to
  create a replication bubble
• An enzyme called primase is responsible for
  initiating replication it joins RNA nucleotides
  to create a primer which is required for DNA
  polymerase to proceed
• Replication then proceeds in both directions
  along the DNA strand until the molecule is
  copied.

http//oak.cats.ohiou.edu/ballardh/pbio475/Heredi
ty/DNA-replication.JPG
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Replication DNA - DNA

• DNA polymerase (enzyme) catalyzes the elongation
  of the new DNA at the replication fork.
• There are dozens more enzymes and proteins
  involved in the replication process
• DNA polymerase also adds nucleotides to the
  polypeptide chain one by one, and each nucleotide
  loses two phosphate groups, which are
  subsequently hydrolyzed in an exergonic reaction
  to fuel the polymerization process

http//oak.cats.ohiou.edu/ballardh/pbio475/Heredi
ty/DNA-replication.JPG
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Replication DNA - DNA

• The strands of DNA are antiparallel their
  sugar-phosphate backbones run in opposite
  directions
• This means replication occurs continuously along
  one strand (leading strand) and discontinuously
  along the other strand (lagging strand)

http//oak.cats.ohiou.edu/ballardh/pbio475/Heredi
ty/DNA-replication.JPG
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Replication DNA - DNA

• The lagging strand is synthesized in separate
  pieces called Okazaki fragments
• The fragments are then sealed by the enzyme DNA
  ligase

http//oak.cats.ohiou.edu/ballardh/pbio475/Heredi
ty/DNA-replication.JPG
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Replication Proof Reading

• The specificity of base pairing
• A T and C G
• Mismatch repair
• special repair enzymes fix incorrectly paired
  nucleotides
• Excision repair incorrectly paired nucleotides
  are excised by a ligase, nuclease, and the gap
  left over is filled in with correct nucleotides
  by DNA polymerase

people.bath.ac.uk/pr1cemb/DNAdamage.htm
http//fig.cox.miami.edu/Faculty/Dana/mismatchrepa
ir.jpg
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Replication Proof Reading

• DNA polymerase can only add nucleotides to the 3
  end of a molecule would mean that it would have
  no way to complete the 5 end of the molecule
  thus linear chromosomes of eukaryotes utilize an
  enzyme called telomerase which catalyzes the ends
  of the molecules called telomeres

http//stemcells.nih.gov/StaticResources/info/scir
eport/images/figurec2.jpg
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Replication Animations

• http//www.lewport.wnyric.org/JWANAMAKER/animation
  s/DNA20Replication20-20long20.html
• http//www.ncc.gmu.edu/dna/mRNAanim.htm
• http//www.csuchico.edu/jbell/Biol207/animations/
  transcription.html
• http//www.johnkyrk.com/DNAreplication.html

http//www.molbio.uoregon.edu/pvh/images/DNARfork
.gif
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Making Proteins

• DNA Replication
• Transcription
• Translation

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DNA
RNA
DeoxyriboseNucleic Acid
RiboNucleic Acid
AT GC
AU GC
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DNA
RNA
How alike?

• -Adenine, Guanine, Cytosine
• have a Polymerase

How Different?
With regards to
In the Cytosol

In the Nucleus__
Location Shape Nitrogen Bases
Sugar Enzymes Used Different Forms Function
Single Helix
Double Helix
A, T, C, G
A, U, G, C
Ribose
Deoxyribose
RNA Polymerase
DNA Polymerase
mRNA, tRNA, rRNA
DNA
Used to make Proteins
Genetic Inheritance
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Replication Original DNA Strand
TACCGGAATCGAGTA Complimentary DNA strand (new
strand)
ATGGCCTTAGCTCAT
Transcription Original DNA Strand
TACCGGAATCGAGTA mRNA Strand
AUG
GCC
UUA
GGU
CAU
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Transcription DNA - RNA
Definition When DNA makes RNA

• RNA polymerase adds RNA nitrogen bases to the DNA
  molecule
• RNA and DNA strands separate.
• The RNA leaves the nucleus, travels through the
  cytosol and
• enters the Ribosome.

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Transcription DNA - RNA
http//www.geneticengineering.org/chemis/Chemis-Nu
cleicAcid/Graphics/Transcription.gif
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Transcription DNA - RNA

• Polymerase Binding and Initiation

A. Promoters specific region of DNA where RNA
polymerase II initiates RNA
transcription i.e. TATA box
B. Transcription Factors aid promoters in
finding promoter regions
C. Polymerase II binds and separates DNA strands
http//www.geneticengineering.org/chemis/Chemis-Nu
cleicAcid/Graphics/Transcription.gif
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Transcription DNA - RNA

• 2. Elongation

• RNA polymerase II moves along strand untwists,
  separates
• DNA strands, exposes 10 bases for pairing at a
  time 5 ? 3

• RNA peels away 10 pairs, rate of 60 nucleotides a
  second

C. Polymerase may transcribe one after another
like a convoy -allows large production of
that protein
http//www.geneticengineering.org/chemis/Chemis-Nu
cleicAcid/Graphics/Transcription.gif
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Transcription DNA - RNA
3. Termination
A. Termination Signal specific DNA region where
RNA polymerase B. Marks end of the gene (1
gene 1 polypeptide) AGTTCCAATAC DNA
Template for brown hair color UCAAGGUUAUG mRNA
for brown hair color Will produce 1 polypeptide
http//www.geneticengineering.org/chemis/Chemis-Nu
cleicAcid/Graphics/Transcription.gif
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Transcription Animations

• http//nobelprize.org/educational_games/medicine/d
  na/b/transcription/transcription_ani.html

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Bacteria No further Processing
www.ou.edu/class/pheidole/bacteria.html
Eukaryotes RNA Processing TO Be Continued.
http//www.bio.miami.edu/dana/104/eukaryote.jpg
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Products of Transcription
1. mRNA Messenger RNA Made of RNA
nucleotides, moves genetic information from
the Nucleus to the cytosol of the cell. 2. tRNA
Transfer RNA Moves Amino Acids (floating in
the cytosol) to the Ribosome 3. rRNA
Ribosomal RNA and Proteins Makes up the
ribosome
ernaehrungs-city.de/zelle-lv2b.htm
http//ghs.gresham.k12.or.us/science/ps/sci/ibbio/
chem/nucleic/chpt15/tRNA.gif
Relationships
http//gears.aset.psu.edu/viz/services/projectlist
/cell/Text/Gifs/ribosome.gif
Anticodon (three nucleotides on tRNA) pair up
with Codon (three nucleotides on mRNA) at the
Ribosome.
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tRNA Structure

• tRNA
• Single RNA strand that folds back on itselF
• Cloverleaf shape when flattened out
• 3 end Amino Acid Attachment
• Anticodon end 1 tRNA matches with 1 specific
  mRNA sequence
• Aminoacyl-tRNA synthetase
• enzyme that matches amino acid to tRNA 3 end
• 1 enzyme exists for every amino acid

http//ghs.gresham.k12.or.us/science/ps/sci/ibbio/
chem/nucleic/chpt15/tRNA.gif
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tRNA Structure
http//www.geneticengineering.org/chemis/Chemis-Nu
cleicAcid/Graphics/tRNA.jpg
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Making Proteins

• DNA Replication
• Transcription
• Translation

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Translation RNA - Protein
A. mRNA leaves the nucleus and moves to the
ribosome in in the cytosol B. tRNA transports
the free floating Amino Acids the cytosol to the
ribosome C. tRNA with an anticodon sequence
binds to the mRNA codon Sequence and produces an
amino acid i.e. tRNA-AAA rRNA-UUU
phenylalanine D. The amino acid is then added
to the growing polypeptide in the Order of the
mRNA sequence
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• Initation
• A. Small ribosomal subunit binds to mRNA
  and tRNA

B. tRNA binds to initiation codon AUG (site P
filled)
C. Large Ribosome unit binds
D. Initiation Factors bind 4 parts together
Translation
http//staff.jccc.net/PDECELL/proteinsynthesis/tra
nslation/steps.html
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2. Elongation

• Codon Recognition
• Codon and anticodon form hydrogen bonds
• tRNA moves to Site A

Translation
B. Peptide Bond Formation Large ribosome
catalazes peptide bond between Amino Acids
from site P and Site A Amino Acid is no
longer attached to site P tRNA
http//staff.jccc.net/PDECELL/proteinsynthesis/tra
nslation/steps.html
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C. Translocation tRNA in P site leaves
ribosome tRNA in site A moves to site P
codon and anticodon keep hydrogen bond and
move as a unit 5 ? 3 (60 milliseconds)
Translation
http//staff.jccc.net/PDECELL/proteinsynthesis/tra
nslation/steps.html
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http//staff.jccc.net/PDECELL/proteinsynthesis/tra
nslation/steps.html
3. Termination
Translation

• Termination codon reaches site A of Ribosome
• -UAA, UAG, UGA
• -do not code for amino acids, only stop
  translation
• B. Release factor binds to termination codon in A
  site
• -causes ribosome to add water moleculeto
  peptide chain
• -hydrolyzes polypeptide from tRNA in site P
  and frees
• polypeptide
• -large and small ribosome units seperate

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Translation mRNA to Amino Acids
bioweb.uwlax.edu
http//www.geneticengineering.org/chemis/Chemis-Nu
cleicAcid/Graphics/Code.gif
bioweb.uwlax.edu/.../Translation/translation.htm
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Translation Animations

• http//highered.mcgraw-hill.com/sites/0072437316/s
  tudent_view0/chapter15/animations.html
• http//nobelprize.org/educational_games/medicine/d
  na/b/translation/translation_ani.html
• http//nobelprize.org/educational_games/medicine/d
  na/a/translation/translation_animation.html

library.thinkquest.org/.../RNA.htm
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http//ghs.gresham.k12.or.us/science/ps/sci/ibbio/
chem/notes/chpt3/proteinlevels.gif
Amino Acid ? Polypeptide ? Protein
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Blast from the Past

• Hippie Protein Synthesis
• http//www.youtube.com/watch?vu9dhO0iCLww

This truly classic, psychedelic-era video was
created by the chemistry department of, and
filmed at, the University of California, San
Diego in 1971. Stanford is in northern California
- too much cool, damp weather to be loose enough
to make something as trippy as this.
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Protein Structure
CCUPro
1 triplet code (Codon) makes up 1 Amino Acid
20 Types of Amino Acids make up proteins
Figure 16.5
-redundancy and no ambiguity
1 polypeptide may consist of hundreds or
thousands of the 20 Amino Acids in a particular
sequence
The sequence of the Amino Acids determines how
the polypeptides Twist and fold into a three
dimensional structure of the protein
The Protein structure determines the Protein
Function
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Eukaryotes vs Prokaryotes

• http//highered.mcgraw-hill.com/sites/0072437316/s
  tudent_view0/chapter15/animations.html
• http//nobelprize.org/educational_games/medicine/d
  na/index.html (advanced main page for previous
  animations replication to translation)