Gene regulation in prokaryotes and eukaryotes

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Gene regulation in prokaryotes and eukaryotes

• Year 13

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Enzymes

• Are biological catalysts.
• Speed up the chemical reactions in living
  organisms.
• Without enzymes, the chemical reactions of life
  would proceed so slowly that life would be hardly
  possible.
• Are not used up or changed by the reaction.

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What are enzymes made of?

• Chemically, enzymes are proteins.
• Because of the unique shape of each enzyme it is
  specific to a particular reaction it will
  catalyse only one reaction.
• There are, therefore, thousands of different
  enzymes in any living organism.

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Some definitions

• Substrate the chemicals an enzyme acts on.
• Active site the part of the enzyme where the
  substrate binds and where the reaction occurs.
  The active site has a specific shape so only
  specific substrates can bind.
• Nomenclature ase

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How do enzymes work?
2 models lock and key induced fit See page
95 Biozone
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Metabolism

• Is all the chemical reactions that occur in the
  cell of an organism.
• Metabolism is made up of all the different
  processes an organism needs to maintain itself
  such as growth, energy, repair, and excretion.
• These processes are a complex network of
  metabolic pathways which are controlled by
  enzymes.

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The importance of enzymes in metabolic pathways.

• A metabolic pathway is a series of steps from a
  starter molecule, resulting in the formation of a
  different end product. Many intermediate
  compounds can be formed in the pathway.
• Each step in the pathway is controlled by an
  enzyme.
• A faulty enzyme can cause metabolic disorders.

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Metabolic pathways can be anabolic produce
large molecules from smaller ones or catabolic
break large molecules into smaller ones.
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Phenylalanine
Enzyme A
Melanin
Thyroxine
Tyrosine
Enzyme B
Enzymes
Enzyme C
Hydroxyphenylpyruvic acid
Enzyme D
Metabolism of phenylalanine
Homogentisic acid
Enzyme E
Maleyacetoacetic acid
Enzyme F
Do exercises Page 97 and 98
CO2 and H2O
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Control of gene expression in metabolic pathways

• Gene expression of enzymes in a metabolic pathway
  must be tightly controlled so the cell has the
  correct amount of each enzyme it requires.
  Control often occurs at transcription.
• Some genes are induced they are only switched
  on in certain situations.
• Other genes are transcribed continuously because
  their products are always needed eg genes coding
  for respiratory enzymes.

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Gene regulation

• Two types of genes
• Structural genes encode specific proteins
• Regulatory genes control the level of activity
  of structural genes ie. Control structural gene
  expression.

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Gene regulation in prokaryotes

• In prokaryotes, operons control the rate of
  transcription.
• An operon is a group of genes that work together
  and code for the enzymes regulating a particular
  metabolic pathway.

Structural gene B
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Structure of the operon

• The operon in prokaryotes comprises a number of
  different features
• Structural genes code for particular enzymes in
  a metabolic pathway
• Promoter gene recognition site for the RNA
  polymerase to bind to.
• Operator gene controls the production of mRNA
  from structural genes.

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INDUCTION
If a substrate is uncommon the bacteria will not
need the enzymes most of the time. So the
repressor is usually attached. This prevents RNA
polymerase from forming mRNA. Therefore no
enzymes. When the substrate molecule is present
some of it acts as an inducer it binds to the
repressor, changing its shape so it cant bind to
the DNA. Transcription takes place.
See this movie on the Lac operon in E. coli for
more detail
Inducer
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REPRESSION
When a substrate is normally present the enzyme
should be normally operating. The only time this
should stop is when the end product levels build
up too much. The repressor cannot bind to the
operator. Some of the excess product acts as an
effector, which helps the repressor to
bind. Transcription is stopped.
See this movie on the Tryp operon in E. coli for
more detail
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http//www.sumanasinc.com/webcontent/anisamples/ma
jorsbiology/lacoperon.html
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Lac Operon - induction
Lactose binds to the repressor protein.
Lactose present- acts as an inducer.
Lac gene off (normal state)
Repressor cant bind to the operator.
Repressor molecule binds to operator and prevents
transcription by RNA polymerase
RNA polymerase binds . Lac gene on. Structural
proteins made.
Lactose all used up.
Tryptophan operon - repression
Effector and repressor molecule bind to the
operator gene and prevent transcription by RNA
polymerase.
Tryptophan accumulates in excess. Some of it
acts as an effector and activates the repressor
molecule.
Tryp gene on (normal state)
RNA polymerase binds
Tryptophan doesnt bind to the repressor which
then cant bind to the operator.
Tryptophan levels in cells decrease, no excess.
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Gene regulation in prokaryotes - summary

• Genes for a metabolic pathway are linked together
  in operons with a common switch mechanism
  (operator).
• No introns no RNA processing
• The structural genes undergo transcription and
  translation simultaneously.
• Regulation occurs by switching all genes of a
  pathway on or off.

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Gene regulation in eukaryotes

• Genes for metabolic pathways in eukaryotic cells
  are separated, not grouped as operons.
• The genes for a metabolic pathway are switched on
  separately.
• Genes have introns that are removed in RNA
  processing.
• Eukaryotic genes have a relatively large number
  of control elements.

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Regulatory DNA regions

• Eukaryotic genes have a promoter region upstream
  of the coding region, where RNA polymerase binds.
• There are 2 two types of regulatory sequences
  that effect transcription of the structural gene
• 1) enhancer
• 2) silencer
• These are located upstream, downstream or within
  the gene (in introns).

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Enhancer sequences

• These are non-protein-coding sections of DNA that
  help regulate transcription by binding proteins
  called transcription factors.
• Silencer sequences
• These are non-protein-coding sections of DNA that
  help regulate transcription by binding proteins
  called repressors.

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Transcription factors

• Two types
• 1) Activators these are small proteins that
  bind to enhancer sequences or RNA polymerase.
  They cause an increase in transcription.
• 2) Repressors these are small proteins that
  bind to silencer regulatory genes. They cause a
  decrease in transcription.

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Role of Transcription Factors
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• Eukaryotic RNA polymerase cannot, on its own,
  initiate transcription.
• It depends on transcription factors to recognize
  and bind to the promoter.
• Transcription factors also bind to the enhancer
  sequence of DNA

RNA polymerase
Transcription factors that bind to RNA polymerase
Transcription factors (activators) that bind to
the enhancer
Promoter region of DNA
Coding region of gene
Enhancer sequence of DNA
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Activating Transcription
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• Transcription is activated when a hairpin loop in
  the DNA brings the transcription factors on the
  enhancer sequence (activators) in contact with
  the transcription factors bound to the RNA
  polymerase at the promoter.
• Protein-protein interactions are crucial to
  eukaryotic tanscription.
• The RNA polymerase can only produce a mRNA
  molecule once the complete initiation complex is
  assembled.

Transcription proceeds until a terminator
sequence is encountered. Then transcription stops.
Enhancer
Promoter
RNA polymerase
Initiation complex
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• http//highered.mcgraw-hill.com/olc/dl/120080/bio2
  8.swf

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DEFECTIVE GENES
Cell division is tightly controlled. If a cells
DNA becomes damaged a gene (p53) within the cell
causes cell division to cease until it is
repaired. Other genes (proto-oncogenes) allows
cell division to begin. If DNA damage is
irreparable or cells get too old they self
destruct, called apoptosis. If damage occurs in
either of the 2 genes mentioned above the cell
will grow at an uncontrolled rate, or become
effectively immortal. These cells cease to carry
out normal functioning. If the damage is not too
severe the cells may form a benign tumour. If
many genes are affected the tumour is said to be
cancerous.
Lab manual page 99