Trends in Biotechnology

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Trends in Biotechnology

• Quick Review of Chapter 2 Cellular Processes

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• Eukaryotic and prokaryotic cells, and the major
  organelles of eukaryotic cells.

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Fig. 2.1 Cell structure and organization (a)
Bacteria cell.
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http//en.wikipedia.org/wiki/Cell_28biology29
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Fig. 2.1 (b) Animal cell.
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• Diagram of a typical animal cell. Organelles are
  labelled as follows
• Nucleolus
• Nucleus
• Ribosome
• Vesicle
• Rough endoplasmic reticulum
• Golgi apparatus (or "Golgi body")
• Cytoskeleton
• Smooth endoplasmic reticulum
• Mitochondrion
• Vacuole
• Cytosol
• Lysosome
• Centriole

http//en.wikipedia.org/wiki/FileBiological_cell.
svg
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Fig. 2.1 (c) Plant cell.
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http//commons.wikimedia.org/wiki/FilePlant_cell_
structure.png
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• Structure of the cells macromolecules, and how
  they are constructed Lipids, carbohydrates,
  proteins, and nucleic acids.

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• Two different classes of lipids have fatty acids
  in their structure.

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Fig. 2.2 Triglycerides have a three-carbon-OH
backbone called glycerol with a fatty acid chain
attached to each carbon.
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Fig. 2.2 (b) Phospholipids are structurally
similar to triglycerides except one fatty acid
chain is replaced by a phosphate.
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Fig. 2.2 (c) Phospholipid bilayer
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• Cell membranes are very complex with a
  phospholipid bilayer embedded with proteins,
  carbohydrates, and glycoproteins.

http//commons.wikimedia.org/wiki/FileCell_membra
ne_detailed_diagram_en.svg
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Fig. 2.3 Structure of fatty acids showing the
carbon backbone.
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Fig. 2.4 Monosaccharides, (a) glucose and (b)
fructose shown as both straight-chain and ring
forms. (c) The formation of a disaccharide
from two joined monosaccharides.
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Fig. 2.5 Cellulose, a structural polysaccharide
composed of glucose monomers, found in plant cell
walls.
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Cellulose.
http//commons.wikimedia.org/wiki/FileCellulose-3
D-balls.png
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Fig. 2.6 Chitin, a structural polysaccharide
composed of N-acetyl glucosamine, is found in the
exoskeletons of insects.
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Fig. 2.7 The 20 amino acids used in protein
synthesis.
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• In the above structures, the top circle
  represents the amino acid backbone (H2NCHCOOH),
  with the R group depicted.
• In the case of proline, which is an alpha imino
  acid, rather than an amino acid, the circle
  represents the CHCOOH group, the imino nitrogen
  shown as an element in the proline ring.

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Fig. 2.8 Peptide bond formation between two amino
acids.
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http//commons.wikimedia.org/wiki/FilePeptidforma
tionball.svg
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Fig. 2.9 The four nucleotides of DNA.
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http//commons.wikimedia.org/wiki/FileDNA_chemica
l_structure.svg
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Fig. 2.10 The double-strand structure of DNA
showing the nucleotides, each made of a
deoxyribose sugar, a phosphate, and a
nitrogen-containing base.
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Fig. 2.11 The Watson-Crick model of DNA. Two
strands of a hydrogen bonded DNA double helix
spiraling around a central axis.
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Fig. 2.12 The deoxy-ribonucleotide monomers of
DNA connected by phospho-diester bonds.
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Fig. 2.13 The nucleotide structure of RNA.
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Fig. 2.14 Base pairing, A-T in DNA and A-U in
RNA.
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http//commons.wikimedia.org/wiki/FileDifference_
DNA_RNA-EN.svg
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Fig. 2.15 Transfer RNA showing the anticodon and
3 amino acid binding regions.
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• A different model of transfer RNA.

http//commons.wikimedia.org/wiki/File3d_tRNA.png
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Fig. 2.16 Central dogma of molecular biology.(a)
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Fig. 2.16 Central dogma of molecular biology.(b)
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http//commons.wikimedia.org/wiki/FileRibosome_mR
NA_translation_en.svg
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Fig. 2.17 The stages of nuclear division in a
process called mitosis, and cell division.
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http//commons.wikimedia.org/wiki/FileMitosis.png
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Fig. 2.18 Semiconservative replication of DNA.
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• Semiconservative replication of DNA showing the
  direction of replication.

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• Some proteins involved in DNA replication.

http//commons.wikimedia.org/wiki/FileDNA_replica
tion_en.svg
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• Show video DNA Replication Process - Free Science
  Videos and Lectures
• http//www.freesciencelectures.com/video/dna-repli
  cation-process/
• Show video Mechanism of Replication
• http//www.dnalc.org/resources/3d/04-mechanism-of-
  replication-advanced.html

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Fig. 2.19 Bidirectional replication of DNA in
(a) prokaryotes and (b) eukaryotes.
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Fig. 2.20 Replication of DNA at a replication
fork in bacteria.
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Fig. 2.20 Replication of DNA at a replication
fork in bacteria.
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Fig. 2.20 Replication of DNA at a replication
fork in bacteria.
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Fig. 2.21 A DNA replication bubble showing the
direction of replication in the two replication
forks, leading and lagging strand synthesis, and
Okazaki fragments in the lagging strand.
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• After replication the DNA might be coiled in
  Eukaryotes
• http//www.freesciencelectures.com/video/molecular
  -biology-visualization-of-dna/

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Fig. 2.22 The amino acids arranged according to
their degeneracy.
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Fig. 2.23 Codons read in-frame.
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Fig. 2.24 RNA synthesis. (a) Transcription is
started when RNA polymerase binds to the DNA at
the promoter region.
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Fig. 2.24 (b) The double-strand DNA unwinds. (c)
RNA polymerase travels along the DNA template,
nucleotides are added to the growing RNA strand.
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Fig. 2.24 (d) RNA polymerase reaches a
terminator, the RNA transcript is released and
transcription is terminated.
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• Show video TranscriptionAdvancedXvid
• http//vcell.ndsu.nodak.edu/animations/transcripti
  on/movie-flash.htm
• Show video 13-transcription-advanced
• http//www.dnalc.org/resources/3d/13-transcription
  -advanced.html

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Fig. 2.25 A stem-loop structure in the newly
synthesized RNA is one way that transcription is
terminated.
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Fig. 2.26 Conserved sequences in (a) bacterial
promoters
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Fig. 2.26 (b) Conserved sequences in eukaryotic
promoters.
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Fig. 2.27 Enhancement of transcription by an
enhancer element. (a) Low level of transcription
without the effect of an enhancer.
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Fig. 2.27 (b) An enhancer sequence increases the
level of transcription.
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Fig. 2.28 After transcription and formation of a
pre-mRNA in eukaryotic cells, the transcript is
processed.
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• Fig. 2.28 After transcription and formation of a
  pre-mRNA in eukaryotic cells, the transcript is
  processed - a nucleotide with functional groups
  is added to the 5 end (5 cap) and adenine
  nucleotides are added to the 3 end (poly-A tail).

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• Show video mRNAProcessingAdvancedXvid
• http//vcell.ndsu.nodak.edu/animations/mrnaprocess
  ing/movie-flash.htm
• Show video 24-mrna-splicing http//www.dnalc.org/r
  esources/3d/24-mrna-splicing.html
• Show video mRNA Splicing
• http//vcell.ndsu.nodak.edu/animations/mrnasplicin
  g/movie-flash.htm

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Fig. 2.29 The three types of RNA (rRNA, mRNA,
tRNA) and their role in protein synthesis.
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Fig. 2.30 Ribosome structure.
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http//commons.wikimedia.org/wiki/FileRibosome_mR
NA_translation_en.svg
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Fig. 2.31 a) Translation initiation.
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Fig. 2.31 b) Translation initiation.
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Fig. 2.31 c) Translation initiation.
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Fig. 2.32 a) b) Elongation during translation.
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Fig. 2.32 c) d) Elongation during translation.
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Fig. 2.32 e) Elongation during translation.
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• Show video 16-translation-advanced
• http//www.dnalc.org/resources/3d/16-translation-a
  dvanced.html
• Show video TranslationAdvancedXvid
• http//vcell.ndsu.nodak.edu/animations/translation
  /movie-flash.htm

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• Regulation of Gene Expression.
• The cell only makes what is needed and controls
  the production of products.
• Both prokaryotes and eukaryotes control the
  stopping and starting of transcription.
• Prokaryotes can lower the rate of translation.

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• Prokaryotic Gene Expression.
• Bacteria use signals called inducers to turn
  genes on or off in response to environmental
  changes.
• Usually these are in the form of a group of
  genes, with a promoter (called an operon).
• There are two major operons that are well known
  in bacteria.

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• Operons have several parts
• Promoter.
• Several structural genes, all controlled by the
  promoter.
• Repressor binding site, called an operator,
  which overlaps the promoter.
• Repressor genes encode for repressor proteins,
  which bind to the operator to block RNA
  polymerase.

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Fig. 2.33 A prokaryotic operon.
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• The lac Operon of E. coli
• Contains three operon genes
• lacZthe enzyme beta-galactosidase, which breaks
  down lactose.
• lacYthe enzyme permease.
• lacAthe enzyme acetylase.

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Fig. 2.34 Regulation of the lac operon. (a) When
the active repressor binds to the operator in the
absence of lactose, RNA polymerase cannot bind to
the promoter and transcription is blocked.
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Fig. 2.34 Regulation of the lac operon in the
presence of lactose. (b) Lactose inactivates the
repressor which releases from the operator, RNA
polymerase binds to the promoter and
transcription starts.
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• Without lactose, the lac repressor, encoded by
  the lacI gene, binds to the operator, keeping RNA
  polymerase from binding to the promoter.
• When lactose is present, it attaches to the
  repressor which changes its shape and releases
  from the promoter.
• Ribosomes immediately attach to the mRNA and
  start translation.
• This is negative control - genes are not
  transcribed when the repressor is bound to the
  promoter.

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• Video LacOperonAdvancedXvid http//vcell.ndsu.nod
  ak.edu/animations/lacOperon/index.htm
• Video Operon Lac
• http//www.youtube.com/watch?vaEtuaEe0C-INR1
• (web Animation The lac Operon
• http//bcs.whfreeman.com/thelifewire/content/chp13
  /1302001.html )

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• The lac operon can also be regulated to allow for
  more transcription
• If glucose is absent, the amount of a molecule
  called cyclic AMP (cAMP) increases inside the
  cell.
• cAMP binds to a cAMP binding protein (CAP), which
  binds near the promoter region. This increases
  lac operon transcription.
• cAMP is lower when glucose is present, and CAP is
  not active.

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• The trp Operon regulates the production of the
  amino acid tryptophan.
• It has several parts
• (a) Promoter.
• (b) Operator gene overlapping the promoter
  region.
• (c) Five genes encoding enzymes that catalyze
  the last steps of tryptophan synthesis.

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• The repressor is inactive unless tryptophan binds
  to it. The activated repressor attaches to the
  operator and blocks transcription.
• If there is no tryptophan, the repressor cannot
  bind and transcription occurs.
• Genes are repressed to avoid too much tryptophan
  production.

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Fig. 2.35 The trp operon showing the five
structural genes and the promoter region.
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• Web Video of trp Operon look at
  http//bcs.whfreeman.com/thelifewire/content/chp13
  /1302002.html

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• Eukaryotic Gene Expression is much more
  complicated than in prokaryotes.

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• Eukaryotic cells regulate gene expression by
• Regulating transcription of genes.
• Controlling mRNA processing.
• Controlling transport of mRNA to the cytoplasm.
• Regulating the rate of translation.
• Controlling availability of mRNA.
• Protein processing.

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Fig. 2.36 Transcription and translation in a
eukaryotic cell.
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Fig. 2.37 Summary of some of the multiple levels
of eukaryotic gene regulation.
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• Transcriptional control
• There are more promoters and regulatory sequences
  in eukaryotic cells.
• Proteins called transcription factors interact
  with the promoter and RNA polymerase, forming the
  transcription initiation complex.
• Gene-specific regulatory proteins bind to special
  DNA control sequences that contain regulatory
  protein binding sites.
• Control sequences can be adjacent to or distant
  from structural genes.
• Individual or distant genes often must be
  regulated in scattered groups or networks,
  sometimes on different chromosomes.

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• Video mRNAProcessingAdvanced
• http//vcell.ndsu.nodak.edu/animations/mrnaprocess
  ing/index.htm

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• Regulation of RNA processing and transport out of
  the nucleus to the cytoplasm
• Different cell types may process the same mRNA
  differently, by a process called alternative
  splicing, to yield different proteins (Figure
  2.38)
• The pre-mRNA for the hormone calcitonin
  (non-processed mRNA) contains five introns
  separating six exons.
• The transcript can be processed to generate
  calcitonin mRNA in thyroid cells or calcitonin
  gene-related peptide (CGRP) mRNA in hypothalamus
  cells.

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Fig. 2.38 An example of alternative splicing to
yield two different mRNAs, calcitonin mRNA in
thyroid cells and calcitonin gene-related peptide
(CGRP) mRNA in hypothalamus.
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• Video mRNASplicingAdvancedXvid
• http//vcell.ndsu.nodak.edu/animations/mrnasplicin
  g/index.htm

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• Translational control
• Influences the final synthesis of a protein
  product (translation).
• Translation is controlled by protein initiation
  factors and proteins that repress (inhibit)
  translation.
• How quickly mRNA degrades influences when mRNA
  can be translated.

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• Posttranslational control is the changing of
  protein products after they are made.

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• Methods of changing them include
• Protein folding and assembly with other proteins
  after synthesis.
• The removal of amino acids.
• Cleavage of the molecule, which is called
  proteolysis.
• Modification of the protein molecule.
• Addition of a sugar is called glycosylation.
• Addition of a phosphate is called
  phosphorylation.
• Importing proteins into organelles.
• Protein degradation.

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• Video ProteinModification
• http//vcell.ndsu.nodak.edu/animations/proteinmodi
  fication/index.htm
• Note this is some of the protein changes in the
  Golgi body. There are many more different types
  of changes possible in other parts of the cell.

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• Draw and label a diagram of the Central Dogma
  of molecular biology.
• On the diagram, show the ways that the flow of
  information in the cell can be regulated in
  eukaryotic cells, beginning at the DNA level and
  ending at the protein level.