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Regulation of Gene Expression. Bacterial Gene Regulation Eukaryotic Gene Regulation. Operons-the basic concept of Prokaryotic Gene Regulation. Regulated genes can be switched on and off depending on the cell’s metabolic needs

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Regulation of Gene Expression

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Regulation of Gene Expression

  • Bacterial Gene Regulation

  • Eukaryotic Gene Regulation


Operons-the basic concept of Prokaryotic Gene Regulation

  • Regulated genes can be switched on and off depending on the cell’s metabolic needs

  • Operon-a regulated cluster of adjacent structural genes, operator site, promotor site, and regulatory gene(s)


Operon

  • Structural gene-gene that codes for a polypeptide

  • Promoter region-controls access to the structural genes, located between the promoter and structural genes, contains the operator site.

  • Operator Site -region where the repressor attaches

  • Regulatory genes-codes for repressor proteins

  • Polycistronic mRNA-transcript for several polypeptides


Repressible Operons

Genes are initially ON

Anabolic pathways

End product switches off its own production

Inducible Operons

Genes are initially OFF

Catabolic pathways

Switched on by nutrient that the pathway uses

Repressible vs. Inducible Operonstwo types of negative gene regulation


trp: a repressible operon


lac: an inducible operon


Videos and Websites

  • http://www.dnatube.com/

  • http://vcell.ndsu.nodak.edu/animations/lacOperon/index.htm

  • http://www.youtube.com/watch?v=VNok-vF03aI&feature=related

  • http://www.youtube.com/watch?v=x_dve8YMtrM&feature=related


An example of positive gene regulation-cAMP

  • cAMP exerts positive control

  • Binds to promoter, stimulating transcription

  • Dependent on glucose concentration


Eukaryotic Genomes:Organization, Regulation, and Evolution

The structure of chromatin

Genome organization at the DNA level

The control of gene expression

Nucleosomes –basic unit of packing, made of two sets of four histones, may control gene expression


The Structure of Chromatin

  • DNA complexed with protein forms chromatin

  • diffuse during interphase

  • condensed during mitosis, forms chromosomes

  • histones and nucleosomes


The structure of Chromatin

  • Based on successive levels of DNA packing


The structure of Chromatin (2)

  • Six nucleosomes/turn, forms a cylinder

  • Higher level of DNA packing: looped domains (20,000 to 100,000 nucleotides)

  • Heterochromatin remains highly condensed during interphase (Barr bodies)

  • Euchromatin able to be transcribed during interphase


Heterochromatin: highly condensed during interphase, not actively transcribed

Euchromatin: less condensed during interphase, able to be transcribed

Types of Chromatin


The Code Beyond Genetics in DNA

  • The original code is that each codon specifies a particular amino acid and subsequent protein

  • The second code is determined by the placement of the nucleosomes.

  • Nucleosomes protect and control access to the DNA


Nucleosomes

  • 30,000,000 nucleosomes in each human cell

  • DNA wraps 1.65 times around a nucleosome

  • The DNA twist is 147 base pairs

  • The average DNA strand contains 225 million base pairs

  • Made of proteins called histones


How do Nucleosomes Function?

  • Bind to the DNA at specific sequences

  • Prevent transcription factors from attaching and initiating transcription

  • Nucleosomes can and do move, letting DNA open to be transcribed. How?

    This has not yet been determined!


The Control of Gene Expression

  • Only a few genes are active at any time-differential gene expression

  • Control can be exerted at any step in the pathway.

  • Chromatin modifications affect availability of genes for transcription


Transcriptional regulation via Chromatin modification

  • DNA methylation-methyl groups added to cytosine-inactivate genes

  • Histone acetylation- -COCH3 added to amino acids. Reduce binding between DNA and histone-consequence?


Websites and Videos

  • http://www.youtube.com/watch?v=eYrQ0EhVCYA&NR=1

  • http://www.youtube.com/watch?v=OEWOZS_JTgk&feature=related

  • http://www.biostudio.com/c_%20education%20mac.htm


Transcriptional regulation at Initiation

  • Role of transcription factors- act as activators and/or repressors

  • Coordinately controlled genes-spatially different than prokaryotes, no operons

  • Examples: heat shock response, steroid hormone action, cellular differentiation


Control at the transcriptional level

  • Transcription Factors-augment transcription by binding to DNA or to each other. Act as repressors and activators.

  • Coordinately controlled genes-usually associated with a specific regulatory sequence and activated or repressed by the corresponding transcription factor


Posttranscriptional Mechanisms

  • Regulation of mRNA degradation: several hours or even weeks

  • protein processing and degradation: activation may require addition of phosphate groups or sugars; use of signal sequences; marking for destruction

  • control of translation: inactivation of initiation factors, use of repressor proteins


Posttranscriptional Mechanisms

  • May be stopped or enhanced at any posttranscriptional step

  • Role of the nuclear envelope

  • Regulation of mRNA degradation- several hours to several weeks

  • Control of translation- inactivation of initiation factors, use of repressor proteins

  • Protein processing and degradation-may require addition of sugars or phosphates; use of signal sequences; marking for destruction


Posttranscriptional Mechanisms

  • microRNA (miRNA)

  • Function: complementary to mRNA and binds to different regions:

    animal cells3’untranslated region

    plant cells3’UTR and coding regions


The Genetic Basis of Development

From single cell to multicellular organism

Differential gene expression

Genetic and cellular mechanisms of pattern formation


From single cell to multicellular organism

  • Involves cell division, morphogenestis and cell differentiation cell division: increases cell numbers morphogenesis: overall shape of the organism is established cell differentiation: cells become specialized in structure and function

  • development has been studied using model organisms


Differential Gene Expression

  • Different types of cells in an organism have the same DNA

  • Plants are totipotent, cells retain the ability of the zygote to give rise to all differentiated cells

  • Animals are not as plastic, alternative approaches used, nuclear transplantations such as “Dolly”


Determination

  • Different cell types make different proteins

  • role of transcription regulation

  • two sources of cellular instructions for determination: cytoplasmic determinants and neighboring cells


Genetic and Cellular Mechanism of Pattern Formation

  • Pattern Formation: spatial organization of tissues and organs characteristic of the mature organism

  • Plants-continuous process throughout life

  • Animals-restricted to embryos and juveniles


Homologous genes that affect pattern formation


How genes control development(Genetic analysis of Drosophila)

  • Revealed roles of specific molecules that direct position and differentiation

  • Cytoplasmic determinants provide postional information (unfertilized eggs: orientation of anterior-posterior and dorsal-ventral already determined)

  • 1200 genes essential for development, 120 in segmentation


Role of Gradients of Maternal Molecules

  • Hypothesized over 100 years ago

  • Bicoid Gene essential for development of the anterior of a fly, produces mRNA that concentrates in anterior half of unfertilized eggs.

  • Female flies w/out this gene produce embryos lacking front half of embryo

  • Bicoid protein regulate other genes, a domino like effect


Homeotic Genes: What are they?

  • Master regulatory genes that identify specific regions of the body and appropriate placement of appendages

  • contain a sequence of 180 nucleotides called the homeobox

  • identical or similar homeobox sequences have been identified in many other invertebrates, vertebrates, fungi and prokaryotes.


Role of Neighboring Cells-Induction

  • Signaling help coordinate spatial and temporal expression of genes

  • sequential inductions control organ formation

  • results in selective activation and inactivation of genes within target cells


Apoptosis-programmed cell death

  • “suicide” genes- product present continuously

  • depends upon regulating protein activity

  • tadpole tail?

  • Degenerative diseases, cancers-faulty apoptotic mechanisms?


The Molecular Biology of Cancer

  • Genetic changes that affect the cell cycle (viruses, carcinogens)

  • Oncogene-cancer-causing gene

  • Proto-oncogenes- normally code for regulatory proteins controlling cell growth, division, and adhesion


The Molecular Biology of Cancer

  • Result of genetic changes

    -can be random

    -can be caused by viruses or carcinogens

  • Oncogenes: cancer causing genes

  • -formed from proto-oncogenes by DNA movement within the genome; gene amplification, or point mutations

  • changes in tumor-suppressor genes


Proto-oncogenesOncogenes

  • Movement of DNA within the genome

  • Gene amplification

  • Point mutation

    Sometimes suppressor genes that normally inhibit growth can be responsible for cancer


Multiple mutations underlie the development of cancer

  • 15% due to viruses

  • Somatic mutations ( 5-10% of breast cancer)


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