regulation of gene expression bacterial gene regulation eukaryotic gene regulation

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 vs. Inducible Operonstwo types of negative gene regulation

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

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

Types of Chromatin

• Heterochromatin: highly condensed during interphase, not actively transcribed

• Euchromatin: less condensed during interphase, able to be transcribed

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 cells3’untranslated region

plant cells3’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-oncogenesOncogenes

• 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)