Unit 4 Proteins Transcription (DNA to mRNA) Translation (mRNA to tRNA to proteins) Gene expression/regulation (turning genes on and off) Viruses 1

Yesterday’s Exit Ticket Template DNA3’3’TACAATGCATTG__’ Non-Template 5’5’ATGTTACGTAAC__’ mRNA5’AUGUUACGUAAC3’ 1)Fill in the blanks. 2)What is the amino acid sequence corresponding to the DNA and RNA sequences below? 2 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 3

Is the DNA in this cell Different From this one? Or this one? 4

GENE REGULATION What is gene regulation? Turning genes on and off in the right time and place Controlling the quantity of proteins produced 5

GENE REGULATION Why 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? 6

Why do genes need to be regulated? 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) 7

Why do genes need to be regulated? 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 8

Why do genes need to be regulated? 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 9

Examples: different cell types within a human Muscle cells express muscle actin and myosin Hair and nail cells express keratin Blood cells express hemoglobin 10

Today’s Plan What is gene regulation? Why do cells do it? How genes are regulated – Bacteria – Eukaryotes Mechanisms of Development 11

“…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? YE S no need to synthesiz e tryptoph an NO need to synthesize tryptophan express genes for tryptophan synthesis HOW? 12

How can a cell do this, with no “brain” or “intelligence” directing it?  Molecules can act as signals by directly influencing transcription 13

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 14

Sweatblock.com; netropolus.com Negative Feedback If something is present, don’t make more of it! - 15

Gene regulation in bacteria Operator: the “on-off switch” that controls the access of RNA polymerase to the genes Operon: promoter, operator, and genes 16

(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 17

(2) expressing the genes of the operon at the right time 18

(2) expressing the genes of the operon at the right time A system of negative feedback 19

(2) expressing the genes of the operon at the right time 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 20

Today’s Plan What is gene regulation? Why do cells do it? How genes are regulated – Bacteria – Eukaryotes Mechanisms of Development 21

Eukaryotes: Differential Gene Expression Differences between cell types result from differential gene expression (a) Fertilized eggs of a frog (b) Newly hatched tadpole 22

Fig DNA Signal Gene NUCLEUS Chromatin modification Chromatin Gene available for transcription Exon Intron Tail RNA Cap RNA processing Primary transcript mRNA in nucleus Transport to cytoplasm mRNA in cytoplasm Translation CYTOPLASM Degradation of mRNA Protein processing Polypeptide Active protein Cellular function Transport to cellular destination Degradation of protein Transcription In eukaryotes, gene expression can be regulated at many different stages. 23

Fig. 18-6a DNA Signal Gene NUCLEUS Chromatin modification Chromatin Gene available for transcription Exon Intron Tail RNA Cap RNA processing Primary transcript mRNA in nucleus Transport to cytoplasm CYTOPLASM Transcription 24

Fig. 18-6b mRNA in cytoplasm Translation CYTOPLASM Degradation of mRNA Protein processing Polypeptide Active protein Cellular function Transport to cellular destination Degradation of protein 25

How is transcription regulated in eukaryotes? Promoters and introns aren’t the only non-coding regions of DNA! Meet the Enhancers: 26

How is transcription regulated in eukaryotes? Liver enhancerLiver 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 27

How is transcription regulated in eukaryotes? Liver enhancerLiver gene (enzyme) Lens gene (crystallin)Lens enhancer Promoter How does a DNA region control a gene? Through activators specific to each control element Activators are specialized transcription factors (proteins) Control Elements 28

Would you go down this: sfomom.blogspot.com; sabotagetimes.com Without this? 29

Stopped Editing Here 30

Liver enhancerLiver gene (enzyme) Lens gene (crystallin)Lens enhancer Liver cellLens cell Lens activatorsLiver activators Pro. Lens gene ON Liver gene ON Lens gene OFF Liver gene OFF Animation 31

Today’s Plan What is gene regulation? Why do cells do it? How genes are regulated – Bacteria – Eukaryotes Mechanisms of Development – Example of malformed frogs 32

Development 1.Determination and Differentiation 2.Getting the right parts in the right places: Pattern formation 33

embryonic development Zygote 34

(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 determination 35

The process of development: some useful terms 1. Differentiation and determination 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 Cella 36

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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 1. Differentiation and determination 38

(a) Cytoplasmic determinants Two different cytoplasmic determinants Unfertilized egg Sperm Fertilization Zygote Mitotic cell division Two-celled embryo Nucleus 39

(b) Induction by nearby cells Signal molecule (inducer) Chain reaction Early embryo NUCLEUS Signal receptor 1. Differentiation and determination 40

Embryonic precursor cell Nucleus OFF DNA master regulatory gene myoD Other muscle-specific genes OFF has potential to develop into a variety of different cell types 41

OFF mRNA MyoD protein (transcription factor) Muscle cell precursor (determined) Embryonic precursor cell Nucleus OFF DNA Other muscle-specific genes OFF master regulatory gene myoD 42

mRNA muscle proteins Part of a muscle fiber (fully differentiated cell) MyoD Another transcription factor OFF mRNA MyoD protein (transcription factor) Embryonic precursor cell Nucleus OFF DNA Other muscle-specific genes OFF Muscle cell precursor (determined) master regulatory gene myoD 43

Outline 1.Determination and Differentiation 2.Getting the right parts in the right places: Pattern formation 44

Antenna Mutant Wild type Eye Leg How do you get the right tissues/organs in the right places??? 45

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 46

Cytoplasmic determinants in eggs are products of maternal effect genes (a.k.a. egg polarity genes) Unfertilized egg unevenly distributed RNA, proteins (from mother) 47

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 49

 Gradient of bicoid protein determines anterior- posterior axis 50

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 51

Today’s Exit Ticket Describe, in your own words, the role of enhancers and activators in eukaryotic gene regulation. 52