Unit 4 Proteins Transcription (DNA to mRNA) Translation (mRNA to tRNA to proteins) Gene...

Unit 4• Proteins• Transcription (DNA to mRNA)• Translation (mRNA to tRNA to proteins)• Gene expression/regulation (turning genes on and off)• Viruses

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Yesterday’s Exit Ticket

Template DNA 3’ T A C A A T G C A T T G __’

Non-Template 5’ A T G T T A C G T A A C __’

mRNA 5’ A U G U U A C G U A A C 3’

1) Fill in the blanks.2) What is the amino

acid sequence corresponding to the DNA and RNA sequences below?

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Met-Leu-Arg-Asn

Today’s Plan

• What is gene regulation? Why do cells do it?• How genes are regulated

– Bacteria– Eukaryotes

• Mechanisms of Development

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Is the DNA in this cell

Different From this one?

Or this one?

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GENE REGULATIONGENE REGULATIONWhat is gene regulation?

• Turning genes on and off in the right time and place• Controlling the quantity of proteins produced

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GENE REGULATIONGENE REGULATIONWhy do genes need to be regulated?

• Every cell in our body has the same set of genes

• Our body consists of trillions of cells and millions of distinct cell types.

What makes a skin cell different from a liver cell?

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Why do genes need to be regulated?

1. Differentiated structures/organs2. Not all of a single cell’s functions are needed all the

time (e.g. we shouldn’t make insulin constantly)

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1. Differentiated structures/organs

2. Not all of a single cell’s functions are needed all the time (e.g. we shouldn’t make insulin constantly)

3. Waste of energy/molecules to express genes whose products are not needed

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1. Differentiated structures/organs

2. Not all of a single cell’s functions are needed all the time (e.g. we shouldn’t make insulin constantly)

3. Waste of energy/molecules to express genes whose products are not needed

4. Some functions are mutually exclusive; two enzymes may have opposite functions

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Examples: different cell types within a human• Muscle cells express muscle actin and myosin• Hair and nail cells express keratin• Blood cells express hemoglobin

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Today’s Plan




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“…Consider, for instance, an individual E. coli cell living in the...human colon, dependent for its nutrients on the whimsical eating habits of its host” textbook, p. 352

tryptophan present?

tryptophan present?

YES

no need to synthesize tryptophan

no need to synthesize tryptophan

NO

need to synthesize tryptophan

need to synthesize tryptophan

express genes for tryptophan synthesis

express genes for tryptophan synthesis

HOW?HOW?

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How can a cell do this, with no “brain” or “intelligence” directing it?

Molecules can act as signals by directly influencing

transcription

Molecules can act as signals by directly influencing

transcription13

How does this really work?

Example: E. coli regulation of tryptophan

(1) turning multiple genes “on” and “off”(2) doing so at the appropriate times

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Sweatblock.com; netropolus.com

Negative Feedback

If something is present, don’t make more of it!

-

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Gene regulation in bacteriaGene regulation in bacteria

Operator: the “on-off switch” that controls the access of RNA polymerase to the genes

Operon: promoter, operator, and genes

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(2) expressing the genes of the operon at the right time

For the trp operon, RNA polymerase can bind when nothing is bound to the operator

For the trp operon, RNA polymerase can bind when nothing is bound to the operator

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A system of negative feedback

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How do we stop repression?How do we stop repression?

• Binding of tryptophan to repressor is reversible

• Repressor activation/deactivation depends upon relative concentrations of tryptophan and repressor protein

• Binding of tryptophan to repressor is reversible

• Repressor activation/deactivation depends upon relative concentrations of tryptophan and repressor protein

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Today’s Plan




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Eukaryotes:Differential Gene Expression

• Differences between cell types result from differential gene expression

(a) Fertilized eggs of a frog (b) Newly hatched tadpole22

Fig. 18-6

DNA

Signal

Gene

NUCLEUS

Chromatin modification

Chromatin

Gene availablefor transcription

Exon

Intron

Tail

RNA

Cap

RNA processing

Primary transcript

mRNA in nucleus

Transport to cytoplasm

mRNA in cytoplasm

Translation

CYTOPLASM

Degradationof mRNA

Protein processing

Polypeptide

Active protein

Cellular function

Transport to cellulardestination

Degradationof protein

Transcription

In eukaryotes, gene expression can be regulated at many different stages.

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Fig. 18-6a

DNA

Signal

Gene

NUCLEUS

Chromatin modification

Chromatin

Gene availablefor transcription

Exon

Intron

Tail

RNA

Cap

RNA processing

Primary transcript

mRNA in nucleus

Transport to cytoplasm

CYTOPLASM

Transcription

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Fig. 18-6b

mRNA in cytoplasm

Translation

CYTOPLASM

Degradationof mRNA

Protein processing

Polypeptide

Active protein

Cellular function

Transport to cellulardestination

Degradationof protein

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How is transcription regulated in eukaryotes?

Promoters and introns aren’t the only non-coding regions of DNA!

Meet the Enhancers:

http://bja.oxfordjournals.org

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Liver enhancer Liver gene (enzyme)

Lens gene (crystallin)Lens enhancer

Promoter

Meet the Enhancers: • DNA control regions corresponding to a specific gene• Can be upstream, downstream, or in an intron• Comprised of control elements

Control Elements

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Promoter

How does a DNA region control a gene? • Through activators specific to each control element• Activators are specialized transcription factors (proteins)

Control Elements

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Would you go down this:

sfomom.blogspot.com; sabotagetimes.com

Without this?

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Stopped Editing Here

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Liver cell Lens cell

Lens activatorsLiver activators

Pro.

Pro.

Lens gene ON

Liver gene ON

Lens gene OFF

Liver gene OFF

Animation

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Today’s Plan



• Mechanisms of Development – Example of malformed frogs

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Development

1. Determination and Differentiation2. Getting the right parts in the right places:

Pattern formation

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embryonic development

Zygote

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(a) Fertilized eggs of a frog (b) Newly hatched tadpole

one zygote many cell types, tissues, organs

cell division (mitosis), differentiation, morphogenesis

The key is differential gene regulation

1. Differentiation and determination1. Differentiation and determination

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The process of development: some useful terms


When I grow up I will be a heart cell!

Better start making actin and myosin!

Hello, my name is

Celly

Hello, my name is

Celly

You’re a heart cell too! Yay!

Hello, my name is

Celly

Hello, my name is

Cella36

TWO COMPLEMENTARY MECHANISMS of DIFFERENTIATION

• Cytoplasmic Determinants before fertilization, when eggs are made maternally derived

• Inductive Signals once there are multiple cells substance from outside a cell (e.g., signal from nearby cell) influences cell’s gene expression


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(a) Cytoplasmic determinants

Two differentcytoplasmicdeterminants

Unfertilized egg

Sperm

Fertilization

Zygote

Mitoticcell division

Two-celledembryo

Nucleus

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(b) Induction by nearby cells

Signalmolecule(inducer)

Chain reaction

Early embryo NUCLEUS

Signalreceptor


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Embryonicprecursor cell

Nucleus

OFF

DNA

masterregulatory gene myoD Other muscle-specific genes

OFF

has potential to develop into a variety of different cell types

has potential to develop into a variety of different cell types

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OFFmRNA

MyoD protein(transcription factor)

Muscle cell precursor(determined)

Embryonicprecursor

cell

Nucleus

OFF

DNA

Other muscle-specific genes

OFF

masterregulatory gene myoD

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mRNA mRNA mRNA mRNA

muscle proteins

Part of a muscle fiber(fully differentiated cell)

MyoD Anothertranscriptionfactor

OFFmRNA

MyoD protein(transcription factor)

Embryonicprecursor cell

Nucleus

OFF

DNA

Other muscle-specific genes

OFF

Muscle cell precursor(determined)

masterregulatory gene myoD

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Outline

1. Determination and Differentiation2. Getting the right parts in the right places:

Pattern formation

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Antenna

MutantWild type

Eye

Leg

How do you get the right tissues/organs in the right places???

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Pattern Formation: Setting Up the Body Plan

• Pattern formation = development of spatial organization of tissues and organs establishment of major body axes

• Positional information = molecular cues that tell a cell its location

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Cytoplasmic determinants in eggs are products of maternal effect genes (a.k.a. egg polarity genes)

Unfertilized egg

unevenly distributed RNA,proteins (from

mother)

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A closer look at the formation of the anterior-posterior (head-tail) axis:

the bicoid gene

Presence of bicoid protein = “put head here”OR

Lack of bicoid protein = “head does not go here” 48

Cytoplasmic determinants in eggs are products of maternal effect genes (a.k.a. egg polarity genes)

Unfertilized egg

unevenly distributed RNA,proteins (from

mother)

mutation in maternal effect gene

mutation in maternal effect gene

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Gradient of bicoid protein determines anterior-posterior axis

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Today’s Take-Homes:

• Gene expression can be regulated at many stages

• Transcription regulation is a common mechanism

• Eukaryotes use enhancers and activators for differential gene expression

• Protein concentrations from mom’s egg play a key role in development

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Today’s Exit Ticket

Describe, in your own words, the role of enhancers and activators in eukaryotic gene regulation.

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Unit 4 Proteins Transcription (DNA to mRNA) Translation (mRNA to tRNA to proteins) Gene...

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