Regulation of Gene Expression Flashcards
Gene Expression
The process by which information in a gene is made into a functional product (such a protein or RNA)
Gene Regulation
The ability of a cell to control the expression of their genes and gene products
Advantages of Gene Regulation (3)
1) Saves energy
2) Ensures that only certain genes are on when needed (Ex: different cell types, stages of development, in response to environmental change)
3) Allows for cellular differentiation
The main methods for gene regulation are… (5)
1) DNA modification
2) Transcriptional modification (turning on or off)
3) Modification of mRNA levels (degradation)
4) Translational modification
5) Protein level or structure modification
NOTE: Modification of protein structure can alter protein function (such as activating and deactivating)
Metabolic Control
Regulation of synthesis and breakdown of products
Bacteria have 3 main methods of coping with environmental fluctuations:
1) Transcription/Post-Transcription Modification
–> Varies enzyme conc. by regulating # of mRNA produced
2) Translation Modification
–> Varies enzyme conc. by regulation rate of protein synthesis (how much protein is produced)
3) Post-Translation Modification
–> Adjusts the activity of enzymes already present (chemical inhibition/activation)
Cells have many ways of reacting to environmental changes but one form of regulation is generally favored: ______________
Why?
Transcriptional regulation is generally favored
–> This is because it is one of the earlier points in the entire gene expression process that offers a point of control: The earlier the cell intervenes, the more energy it saves!
Tryptophan Biosynthetic Pathway
Involves 5 enzymes in a series of chain reactions
–> Tryptophan (Tpr.) is an amino acid
Tryptophan biosynthesis has multifaceted regulation:
1) Has feedback inhibition where when tryptophan is in excess, it can act as an inhibitor to an early enzyme in its own biosynthetic pathway (allosteric inhibition)
2) Transcriptional regulation: When tryptophan is in excess, it can trigger a response that represses the expression of genes needed to produce the enzymes involved in the tryptophan biosynthetic pathway
–> (transcriptional regulation occurs through operon system in which tryptophan binds to a repressor which sits on the operator)
Transcriptional Regulation
Increasing or decreasing the rate of transcription
–> Impacts the amount of mRNA produced (or other direct gene products) which can then in the case of mRNA impact amount of protein produced
In bacteria, multiple genes are under…
the control of ONE promoter
–> Creates polycistronic mRNA
Due to the grouping of genes in bacteria, they can…
Regulate multiple related genes together/simultaneously
–> Have the ability of coordinate control
Coordinate Control
The regulation of multiple genes together
–> A single “on/off” switch can control a cluster of functionally related genes
Main method of coordinate control in bacteria
Operon Model
Operon
A cluster of genes under the control of a single promoter
Operons consist of:
1) Promoter
2) Related Genes
3) Operator
Promoter
Sequence where RNA polymerase binds
Related Genes
Genes under the control of the same promoter
Operator
Segment of DNA that lies BETWEEN the promoter and the cluster of genes it controls
The operator is similar to an…
“on/off” switch
The operator controls…
The access of RNA polymerase to the genes in an operon, specifically, the start site of transcription
The activity of an operon is regulated/controlled by:
1) Regulatory genes
2) Their encoded regulatory proteins
Regulatory Gene
A gene that encodes regulatory proteins (usually REPRESSORS)
Regulatory genes are constantly…
EXPRESSED (but at a low rate)
Regulatory genes are usually found where?
Far away from the operon it acts upon
Repressor
A regulatory protein that binds to the OPERATOR of an operon, preventing transcription by blocking RNA polymerase from interacting with the genes
Operators fluctuate between two states:
1) Repressor bound
2) Repressor unbound
One of the best characterized operon models
Lactose metabolism in E.coli
Lactose
A disaccharide that can be used for energy by bacteria when glucose is not present (or present in very minimal amounts)
–> NOT the preferred sugar to breakdown
Lactose breaks down into
Galactose and Glucose
What enzyme catalyzes the breakdown of lactose?
Beta-Galactosidase
What bond links glucose and galactose in lactose?
Beta-Galactoside Linkage
Usage of lactose for energy requires…
2 enzymes:
1) Galactoside Permease
2) Beta-Galactosidase
Galactoside Permease
Enzyme that acts as a transport protein in the cellular membrane that allows for the transport/passage of lactose INTO the cell
Beta-Galactosidase
Catalyzes the breaking of the Beta-Galactoside bond; the cleavage of lactose into galactose and glucose
–> Uses water to break the bond (hydrolysis rxn)
The Lac Operon controls the production of…
Galactoside Permease and Beta-Galactosidase
Lac Operon
An INDUCIBLE operon (that controls the genes that encode for lactose metabolism enzymes)
–> Usually “off” (has repressor bound to the operator) but can be induced (“turned on”) in the presence of lactose
Why is the lac operon usually off?
Because it only activates in the presence of lactose and lactose is a pretty rare sugar
(and even when it is present, there are other pathways which prevent the operon from turning on: AKA glucose conc.)
Lac Operon Genes
3 main genes:
1) Lac Z gene
2) Lac Y gene
3) Lac A gene
Lac Z gene
Encodes for Beta-Galactosidase
Lac Y gene
Encodes for Galactoside Permease
Lac A gene
(don’t really need to know)
Encodes for a transacetylase
Lac I gene
Encodes for the lac operon REPRESSOR
What is the regulatory gene for the lac operon?
Lac I gene
Binding sites on the lac operon repressor
Has 2 binding sites:
1) one DNA binding site (to bind to the operator)
2) one “lactose” binding site (to bind the inducer)
–> Not actually a lactose binding site as the inducer isn’t lactose itself but an isomer of lactose
Inducer of the lac operon
Allolactose: An isomer of lactose
When lactose is not present
The lac operon repressor is made and bound to the operator in the lac operon
–> Preventing RNA polymerase from interacting with the genes = no transcription of genes = no production of lactose metabolic enzymes
When lactose IS present
The lac operon is made BUT allolactose attaches to its secondary binding site, changing the repressor’s conformation
–> Change in conformation = repressor cannot bind to the operator (falls off and prevents newly created repressors from binding)
–> RNA polymerase is unblocked and can begin interacting with the genes = transcription begins = production of lactose metabolic enzymes
== LACTOSE BREAKDOWN
What is the secondary regulatory mechanism that prevents lactose breakdown?
Glucose levels
If BOTH glucose and lactose are present…
Lactose WILL NOT be broken down (even if the operon is no longer blocked due to the presence of lactose)
Bacteria sense glucose levels through
cAMP: cyclic AMP
What enzyme produces cAMP?
Adenylyl Cyclase
How does glucose impact cAMP?
It inhibits the production of cAMP
–> Glucose binds to adenylyl cyclase and through this inactivates the production of cAMP from the enzyme
–> Therefore, the more glucose there is, the less cAMP there is
When glucose levels are high, cAMP levels..
Are LOW
Why is cAMP important to the lac operon?
Because it activates CAP
–> A protein needed to increase the binding affinity of RNA polymerase to the lac operon promoter
CAP
Catabolic Activator Protein
What is the relationship between CAP and cAMP?
cAMP is needed to activate CAP
–> Cap must be activated before it can bind to the lac operon promoter
What is the issue with RNA polymerase and the lac operon?
RNA polymerase has a low binding affinity to the lac operon and so it will not bind on its own to the promoter
–> Transcription of lactose metabolic genes therefore can’t occur if it can’t bind
When glucose levels are high,
cAMP levels are ___________ which causes CAP to be ______________ and therefore…
When glucose is high:
cAMP levels are LOW, which causes CAP to be inactive (less cAMP to bind to CAP) and thus won’t bind to the lac promoter
…and therefore, RNA polymerase can’t bind the promoter either and no transcription can occur (no lactose metabolism)
When glucose levels are low,
cAMP levels are ____________ which causes CAP to be ______________ and therefore…
When glucose is low/absent:
cAMP levels are HIGH, which causes CAP to be more activated (more cAMP to bind to CAP) –> Leads to active CAP binding to the lac promoter
and therefore, RNA polymerase binding affinity INCREASES and BINDS to the promoter causing transcription to begin and LACTOSE METABOLISM TO OCCUR
What is the purpose of the secondary regulatory pathway (with cAMP) of the lac operon?
To ensure that when glucose is around, E.coli isn’t wasting energy on creating lactose metabolism enzymes when its breakdown isn’t needed
CAP + cAMP process is not just in the lac operon regulatory process…
It is also found in many other catabolic (sugar breakdown) pathways
All cells have the SAME _________ but differ in their…
1) Have the SAME GENES
2) But they differ in their GENE EXPRESSION
Differential Gene Expression
The selective expression of different genes by cells with the same genome
–> Leads to cell differentiation
Housekeeping Genes
Genes that are expressed in ALL cells at all times
(as they control/encode for fundamental processes of life)
Different types of gene expressions: (3)
1) Genes expressed ALL the time but only in some cell types
2) Genes expressed only at specific times in cell life cycle
3) Conditionally expressed genes (in response to stimulus)
How do we know differential gene expression happens? (What can we analyze)
Analyze DNA of two cell types = See that the sequences are the same
Analyze RNA/Proteins of two cell types = we see that they are drastically different
Stages at which gene expression can be regulated: (7)
1) Chromatin modification
2) Transcription
3) RNA Processing
4) Transport to cytoplasm
5) Translation
6) Protein Processing
7) Transport to cellular destination
Every step of information flow represents…
A point at which gene expression can be regulated
Chromatin Modifications (2)
1) Histone Acetylation
2) DNA Methylation
1st level of DNA packaging
Histones
Octamer
A set of 8 histones that form a complex at the core of a nucleosome
Histones
A group of BASIC (+ charge) proteins around which DNA (- charge) wraps around
What causes DNA wrapping around histones?
An attraction between the positive and negative charges:
(-) DNA is attracted to (+) histones
Nucleosome
Histone octamer with DNA wrapped around it
Histones are rich in…
Which causes…
Arginine and Lysine: Creates the (+) charge of the histones and contributes to their basicity
2 Forms of chromatin organization
1) Heterochromatin (tight)
2) Euchromatin (loose)
Heterochromatin
Tightly condensed form
–> Packed so tightly that transcription machinery cannot access the DNA = “silenced” genes
Where is heterochromatin mostly found?
1) Non-Transcribed DNA regions
2) Ends of chromosome
Euchromatin
Less condensed (looser) state
–> Looser packing = room for transcription machinery to access the DNA = transcription can occur (transcriptional regulatory factors will influence whether it actually does)
Epigenetics
The study of how chromatin can be modified to regulate gene expression (gene regulation at the DNA level)
–> Heritable traits within the life of a cell that do not involve changes in the DNA sequence
Histone Tails
The N-termini of histones that protrude out of the nucleosome
Due to histone tails protruding from the nucleosome:
Histone tails are accessible to various enzymes which catalyze the modification of chemical groups
–> Addition of acetyl groups to amino acids within the tails
Histone Acetylation
The addition of acetyl groups to amino acids in the histone tails (specifically adding to Lysine and Arginine)
What effect does histone acetylation have on histone charge?
Acetylation neutralizes the positive charge of histones == Decreased attraction with DNA
Histone acetylation causes…
Decreased attraction between DNA and histones
== LOOSER wrapping of DNA around histones
= INCREASE IN TRANSCRIPTION
(Allows transcription machinery to access the DNA)
De-Acetylation (of histones)
The removal of acetyl groups (from histones)
–> Causes increased (+) charge of histones which leads to greater attraction with DNA (-)
== Tighter wrapping –> DECREASED TRANSCRIPTION
Enzymes that catalyze acetylation and de-acetylation
Acetylation: HATs (Histone acetyltransferases)
De-acetylation: HDs (Histone De-acetylases)
DNA Methylation
The addition of methyl groups DIRECTLY to the DNA (bases)
In DNA methylation, where do the methyl groups get added?
Most commonly added to CYTOSINE
DNA methylation affects transcription in 2 ways:
1) Causes tighter wrapping of DNA = Decreased transcription
2) Can inhibit binding of TFs to DNA (blocks their binding sites)
Demethylation
The removal of methyl groups from the DNA which LOOSENS wrapping and increases transcription
Methylation is catalyzed by
Methyltransferases
Epigenetic Inheritance
The inheritance of traits transmitted by mechanisms NOT involving DNA sequence itself
Example of Epigenetic Inheritance
Agouti Gene in Mice
Agouti gene
Determines coat color in mice
–> Is normally only expressed during fur development –> Spends most of its time in a methylated (silenced) state
Unmethylated vs Methylated Agouti Mice
Unmethylated (Active agouti gene) = Yellow mice that are obese and prone to diabetes + cancer
Methylated (Silenced agouti gene) = Brown coat, normal weight, generally healthy
Pregnant yellow mouse fed folic acid rich food
High amount of methyl in the food during gestation
–> Produced predominantly brown coated mice that were healthy
–> Changed gene expression led to different phenotype in offspring
Pregnant yellow mouse fed normal diet
Produced predominantly yellow coated mice that were not healthy
–> Passed down an “epigenetic mark”
Control Elements
Segments of non-coding DNA that serve as binding sites for transcription factors
2 types of transcription factors
1) General Transcription Factors
2) Specific Transcription Factors
General Transcription Factors
Act at the promoters of ALL genes (not specific, needed for transcription on a fundamental level)
–> Usually involved in aiding binding of RNA polymerase to the promoter
Specific Transcription Factors
Bind to control elements that may be far or close to the promoter
–> DO NOT bind to the promoter itself
–> consist of activators and repressors
Types of control elements
1) Proximal control elements (close to the promoter)
2) Distal control elements (far from promoter)
Distal control elements
Binding sites for TFs that are FAR from the promoter
AKA Enhancers
Enhancers can be…
Upstream OR downstream of the specific gene
Each enhancer is generally associated with…
only ONE gene
(though one gene may be under the control of multiple enhancers)
Transcription activators binding sites
1) DNA binding site = Allows for binding to the enhancer
2) Activation Site = Binds to general TFs or mediator proteins to help with transcription initiation
Transcription Activators Process
1) Activators bind to the enhancer distal control elements
2) Protein mediated DNA bending occurs bringing the activators close to the promoter
3) Activators bind to general TFs and MPs, helping in the assembly and orientation of the transcription initiation complex
4) Transcription initiates!
Transcription Repressors function in 2 main ways
1) Some bind to the enhancer, physically blocking the binding of activators to the enhancer
2) Interfere with the activators directly which inhibits their binding to the enhancer
Unlike prokaryotes, eukaryotes have…
One promoter for EACH gene
–> All genes have their own promoters
In eukaryotes, related genes are…
NOT clustered together
They can be scattered all over the place
Coordinate control of related genes in eukaryotes depends on…
Each related gene having the same specific common combo of control elements
–> when activators are present in the nucleus, all the related genes are simultaneously activated because they all have the same control elements recognized by the same molecules
External Signals and Transcription
2 methods for external signals affecting transcription:
1) Signal physically enters cell
2) Signal transduction cascade
External signals: steroid hormones
Physically enter the cell, interact with a receptor to create hormone-receptor complex which then enters the nucleus and acts as transcription factor
How do different activators end up in different cell types?
2 main processes
1) Cytoplasmic determinants
2) Induction signals
Cytoplasmic determinants
Maternal substances (RNA/proteins) in the EGG that are UNEVENLY distributed in the egg cytoplasm
== On purpose so that daughter cells have non-identical cytoplasms that contain different activators
Inductive Signals
Due to cells have different cytoplasm contents, cells are sending out different signals that nearby cells pick up
–> If the signal given out/accepted regulate transcription, the signal will get into nucleus in some form and therefore begin transcription
Environment conditions contributes to…
cell differentiation
Methods of post-transcriptional regulation
1) mRNA degradation
2) Initiation of translation
3) Protein processing and degradation
mRNA degradation regulation
The lifespan of mRNA within the cytoplasm can affect how many times a single mRNA gets translated
–> Directly impact amount of a protein produced
What determines mRNA lifespan?
Sequences at the 3’ and 5’ ends of mRNA
(leader and tailer regions)
Initiation of Translation Regulation
Regulatory molecules can bind to the 3’ and/or 5’ UTR regions of mRNA which can block the attachment of ribosomes
–> Can also be regulated through activation/deactivation of translation initiation factors
Post-translational regulation
1) Protein Processing
2) Protein Degradation
Protein processing
After translation, proteins can undergo processing, chemical modifications, that can alter their structure/activate or deactivate them
Ex: Phosphorylation
Protein degradation regulation
The lifespan of a protein is regulated by selective degradation
–> Many proteins need to have a short life cycle
(ex: cyclin and TFs)
Ubiquitination
The addition of small protein ubiquitin to proteins which targets them to the proteasome for degradation
Proteasome
Giant protein complex that binds proteins and degrades them through peptidases
