Regulation of Gene ExpressionCh. 16.1-16.2;16.4-16.5
1 Embryo 200 Cell Types• From a single embryo, 200 types
of cells can be produced (differentiation)
• Diversity comes from genes being turned off
• Expression of the genes lead to specialization of the cell
• Transcriptional regulation controlling the expression of genes
1) post-transcriptional effect mRNA
2) Translational protein translation
3) Post-translational life span/activity of protein
Regulation in Prokaryotes• Adjust biochemistry quickly
as environment changes• Jacob and Monod
extensive studies into the effects of lactose on expression of lactase genes
• Operon regulatory sequence in DNA for a specific gene(s) + the genes
• Regulatory proteins bind to operons to promote or inhibit the transcription of transcription unit (single mRNA coded in the operon)
Regulation of an Operon• Operator section at the
start of the operon• Activator protein
attaches to operator to promote expression
• Repressor protein attaches to operator to inhibit expression
• Gene coding for regulatory proteins (activators/repressors) are called regulatory genes
• Non-regulating proteins come from structural genes
The lac Operon• 3 genes:1) lacZ codes for β-galactosidase;
breaks lactose into glucose + glactose
2) lacY codes for permease; actively transports lactose into the cell
3) lacA codes for transacetylase; We don’t know what it does
• Negatively regulated– Regulator gene lacI codes for Lac
repressor– Limits lac expression when lactose is
absent (normal)– When lactose is added, it is made into
allolactose (inducer for lac operon) – Inhibits lac repressor by binding to it
Lac Operon Part II; Positive Regulation• Lac operon is repressed in the
presence of lactose if glucose is also added. Why?– Glucose is a better source of energy– Converting lactose into usable
sugars (glucose) requires energy• CAP (catabolite activator protein)
activator synthesized in an inactive form; activated by cAMP (produced when glucose is absent)– Active form binds to CAP site at the
lac operon promoter allowing RNA Poly to attach
• If we add glucose, cAMP levels drop so CAP is deactivated and RNA Poly can bind to the DNA
trp Operon and Protein Synthesis• Some proteins, like
tryptophan, must be synthesized when not present to be absorbed
• trp Operon codes enzymes needed to make tryptophan; regulated by trpR (repressor) that is normally inactive; trp operon used to make tryptophan
• When tryptophan levels are high, the repressor is active and trp operon is blocked (repressible operon)
• Tryptophan is a corepressor; activates repressor
Regulation in Eukaryotes• Eukaryotes do not have
operons; regulatory gene are spread across the genome (side effect of variation)
• Eukaryotes use all forms of gene regulation:
1) Transcriptional Regulation
2) Post-transcriptional regulation
3) Translational regulation4) Post-translational
regulation
Transcriptional Regulation• Promoter region of DNA
upstream (~25bp) from the transcription unit– TATA Box 7-bp sequence
5’-TATAAAA-3’• TFs (transcription factors)
recognize TATA and bind to it; then RNA Poly II can bind
• Further upstream are the regulator sequences (promoter proximal elements) in the promoter proximal region
• Regulatory proteins bind here to enhance or repress transcription
Activators and Transcription• RNA Poly II + TFs transcription
initiation complex; not that efficient
• Activators proteins that help the complex attach and start translation
• Activators can be specific (one cell type for one gene) or general (multiple genes in all cell types) which are also called Housekeeping genes
• Enhancer regions on the DNA can increase transcription rate by interacting with activators (act as coactivators) by bending DNA into a loop
Motifs in DNA Binding Proteins• Domains structures in a protein made
from the combination of secondary folding options (helix, sheet, coil)– Ex. Helix-helix-coil-helix
• Motif specialized domains conserved in different types of proteins
• DNA interacting Motifs:1) Helix-turn-helix DNA binding region
of protein2) Zinc Finger finger shape with zinc
ion; bind to DNA grooves3) Leucine zipper dimers held together
by hydrophobic regions; bind to major groove of DNA
Combinational Gene Regulation• Regulation of most genes in more
complex than just activation or repression
• Genes can have multiple activators and repressors
• These regulation points between different genes overlap and follow the stronger influence
• Gene A is regulated by enhancer regions 1, 2 and 3; Gene B is regulated by enhancer 2, 3, and 4– Activators on 2 and 3 will produce A
and B proteins – Repressors on 3, and 4 will limit B
protein a great deal and A proteins a little bit
Coordinated Regulation• Proteins can be
regulated in complex organisms across many types of tissues through chemical signals (hormones)
• Steroid Hormone Response Element region in gene that hormone-receptor complex binds to– Allows regulation in
several cell types very quickly
Methylation of DNA• DNA methylation adding
methyl (-CH3) to cytosine bases– Turn off gene (silencing) by
blocking access to promoter region• Epigenetics change in gene
expression but no change in the DNA itself
• Hemoglobin turned off in all other cell types this way
• Genomic Imprinting silencing of one of two alleles during development– Methylated allele is not expressed
Chromatin Structure• Histones can block access
to DNA and thus regulate it
• Chromatin remodeling changing its structure– Nucleosome remodeling
complex moves histones along DNA or reshapes them to open a region
• Adding Acetyl Groups (CH3CO-) weakens the interactions between the histones and DNA
• Methylation of Histones marks histones wrapped with deactivated DNA
Gene Regulation in Development• Gene regulation is most
important during early development; determine the cell-types and physiology of the organism
• Regulation sensitive to both time (must all happen in the right order and within a certain window) and place (location in embryo determines location in body)
• Understanding comes from our model organisms:– Fruit fly, nematode worm,
zebrafish, and house mouse
From Zygote to Fetus• After fertilization, a zygote
develops into a fetus through several mechanisms
1) Mitosis need lots of cells2) Movement of cells cells need to
form the right shape3) Induction cell of a certain type
needs neighboring cells to respond to get a result
4) Determination totipotent cells becomes specific cell types
5) Differentiation cell types become finalized so tissue and systems can be made
Hold Up Mr. Nucleus…Cytoplasm has something to say…
• Not all regulation of a zygote comes from the nucleus
• Zygote’s cytoplasm is from the egg used at fertilization
• Cytoplasmic determinants– mRNA strands and proteins in
cytoplasm of egg also regulate the zygote
– Not reproduced during cell divisions; First divisions of zygote separate determinants asymmetrically so each daughter as an uncontrolled amount
– Only really take effect during the first few divisions but can last till tissues form
– Inherited only on the maternal side
Induction• Major step in the process of
determination• Signal molecules from very
specific cells (inducers) sent to receptor cells
• Two methods:1) Signal released and travels
short distances to receptors
2) Cell-to-Cell contact between proteins in the membranes of inducers and receptors
Differentiation• Determination narrows the
type of cells possible and differentiation limits to one cell type
• Genes required for cell type are left on while other genes are “turned off”
• Master regulatory genes promote the transcription of proteins needed to specialize the cell– myoD master gene
regulates MyoD transcription factors which promotes skeletal muscle proteins
Physical Position and Regulation• Pattern formation
arrangement of organs in the body– Discovered studying the
effects of mutations on the embryogenesis of fruit flies
– Particular genes control the body plan for all complex organism
• Steps required:1) Determine front, back,
head, and tail (ventral, dorsal, anterior, and posterior) of embryo
2) Divided zygote into segments
3) Use segments to map out body plan
Maternal-Effect Genes• Expressed when egg is
produced by the mother; mRNAs made from the bicoid gene
• Control the anterior-to-posterior polarity of the egg (front to back)
• Bicoid protein is produced and the highest conc. marks the anterior (head) and drops as move along to the posterior (butt) which has the lowest conc.
Segmentation Genes• 24 genes divide embryo
into regions• 3 Types:1) Gap Genes form
segments along A-P axis; broad regions
2) Pair-rule Genes divide broad regions with units of two segments each
3) Segment polarity Genes sets the boundaries for each segment; each segments needs an A-P axis
Homeotic Genes• Genes specify which
segment becomes what; where are the legs, eyes, wings, etc…– Hox genes– 8 Hox genes in fruit flies– Actually occur in order on
chromosome (AP)– Found in all animals and is
highly conserved• Homeo-Box region in all
homeotic genes that codes for its specific homeodomain (TF for its protein)
Genes and Cancer• 2 types of Cancer1) Familial Cancer inherited; common
with breast, colon, and testicular cancers
2) Sporadic Cancer occur randomly; more common form; can happen from viruses altering DNA
• All cancer is a multi-step process; need several key mutations
• 3 Classes of Genes effect cancer frequency:
1) Proto-oncogens2) Tumor suppressor genes3) microRNA genes
– (not covering this)
Proto-Oncogenes• Genes that stimulate cell
division in regular healthy cells• Code for growth factors, signal
receptors, transduction components, and TFs
• When mutated, they can become overactive oncogens
• Only one allele needs mutated to take effect– Mutation in the promoter – Mutation in the transcription unit– Translocation moves gene to a
more active promoter or enhancer
– Virus adds genes that activate or enhance a gene
Tumor Suppressor Genes• Code for proteins that inhibit
cell division• Keep Proto-oncogenes
repressed• TP53 codes for p53 that
inhibits CDKs used to pass the G1/S checkpoint
• If mutated, p53 can’t inhibit division
• p53 mutations are in 50% of all cancers
• Both alleles must be inactive for a tumor suppressor gene to lose function
Homework• Suggested Homework:– Test Your Knowledge Ch.
16• Actual Homework:– Discuss the Concepts #1– Interpret the Data Ch.
16– Design the Experiment
Ch. 16
Assignments for Next Week• PPT Presentations on Ch. 18:
– Groups of 3; 12-15 mins long– Topics:
• DNA Cloning and Building DNA Libraries• Gel Electrophoresis, Southern Blot, Northern Blot, and Western Blot• DNA Cloning and Bacteria Transformation for Protein Synthesis• BLAST Program and How it is Used
• Papers on Ch. 19:– 3 page paper discussing the following:
• Darwin’s Journey• Data and Experiments by Darwin• World Reaction to Darwin’s Theories• Basic Principles of Evolution
– DO NOT answer these section by section. These are the BIG IDEAS you paper must discuss. It should be a summary of Darwin’s life and impact on Biology
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