Ch 15: Regulation of Gene Expression Flashcards
2 levels of a metabolic pathway can be controlled
- cells can adjust the activity of enzymes already present, can be based on supply
- cells can adjust the production of certain enzymes
operon model
control of gene expression in bacteria
nucleoid
In Prokaryotes, bacteria are found in a dense region of DNA called a nucleoid
3 ways genetic recombination in bacteria
- transformation
- transduction
- conjugation and plasmids
Transformation
- Uptake naked, foreign DNA from the surrounding environment, incorporated into it’s genome
- DNA from a cell that has broken open
- Important in biotechnology as a way getting bacteria to make proteins for humans (Insulin and HGH)
Transduction
- Phages carry bacterial genes from one host to another
- **Happens when bacterial DNA is accidentally packed in a capsid**
Conjugation and Plasmids
- Directs transfer of genetic material(sex reproduction), through a pilus
- Must have a segment of DNA called F factor, can be DNA or plasmid(small, circular, self-replicating, separate DNA molecule)
- F Plasmid contains about 25 genes
- Only one bacterium passes along DNA
- Pass either DNA or Plasmid
R Plasmid and Antibiotic Resistance
- Antibiotic Resistance is passed from one bacterium to another by the passing of plasmids
- A plasmid can have up to 10 different resistance genes
Responding to environmental change by regulation gene expression
A bacterium can tune its metabolism to the changing environment and food sources
trp
- naturally, trp operon is on and genes for tryptophan are transcribed
- when tryptophan is present, binds to the trp repressor protein which turns the operon off
- the repressor is only active when its corepressor tryptophan is present, the operon is turned off if the tryptophan levels are high
coordinately controlled
where genes are grouped and they are turned off and on with one switch, E Coli synthesizes the proteins at once
operator
the on-off switch is bounded too by repressor to turn off, positioned within the promoter
operon
operator + promoter + the genes they control, trp operon is naturally turned on
repressor
binds to the operator and blocks the attachment of RNA polymerase to the promoter, prevents transcription of the genes
regulatory gene
codes a repressor protein, upstream from the operon, repressor does not permanently bind since it is reversible, is also allosteric(is inactive and active)
corepressor
cooperates with the repressor to switch an operon off
repressible operon
it can be inhibited when a specific small molecule binds allosterically, trp operon is a repressible operon, anabolic
inducible operon
usually off but is turned on when a specific small molecule interacts with a different regulatory protein, catabolic
inducer
a small molecule that inactivates the repressor
Steps of lac operon reg
- lac operon(inducible) contains genes that code for enzymes for breaking down of lactose
- lac repressor is naturally active and switches the lac operon off
- the inducer(alactose) inactivates the repressor to turn the lac operon on
inducible enzymes
synthesis is induced by a chemical signal(lac)
repressible enzymes
the molecule is added to repress it(trp)
negative control
operons are switched off by the active form of their repressors
activator
a protein that binds to DNA and stimulates transcription of a gene, CRP
cAMP
accumulates when glucose is scarce, activates when bound to CRP
E.Coli using glucose
- E, coli will use glucose when it is present in the environment
- when glucose is scarce, CRO acts as an activator
- this activated CRP attaches upstream near the promoter and facilitates the binding of RNA polymerase to the promoter of the lac operon
- This is positive regulation since CRP binding to the promoter stimulates gene expression
- when glucose levels increase, CRP detaches, and transcription goes at a slow rate
- positive regulation only has to do with the binding of RNA polymerase
differential gene expression
the expression of different genes by cells with the same genome
Where does gene reg happen?
- gene expression often happens in transcription for bacteria
- Eukaryotes can regulate gene expression at multiple points
Regulation of Chromatin Structure
- DNA of EU cells are packed with proteins in a mix called chromatins(makes up nucleosomes(has 8 histones and DNA)), this helps reg gene expression
- heterochromatin is usually not expressed
- The location of a gene promoter relative to its structure can influence gene transcription
- chemical mods to histone proteins and DNA can influence chromatin structure and gene expression
Histone Modifications and DNA Methylation
chemical modes to histones play a role in the reg of gene transcription
histone tail
N-terminus of each histone protein in a nucleosome protrudes out, enzymes modify this
histone acetylation
adds acetyl group to an amino acid/+ lysines in histone tails, promotes transcription by opening up the chromatin structure
histone methylation
adds a methyl group to the histones, condenses chromatin, and reduces transcription
DNA methylation
enzymes methylate the DNA itself, which happens in plants most often, done to make sure some genes are not expressed, the pattern is inherited, tightly packs it, enzymes methylate the correct daughter strands
epigenetic inheritance
inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself, these chromatin mods are just transmitted, mutations in DNA are permanent, mods to the chromatin can be reversed(epigenetic)
Regulation of Transcription Initation
- chromatin-modifying enzymes initially control gene expression by making region of DNA more or less able to bind to the transcription machinery
- once the chromatin is modified for expression. the initiation of transcription initiation in eukaryotes is the next step
transcription initiation complex
assembles on the promoter upstream end of the gene, enhances gene expression
enhancer regions
enhances gene expression
enhancer regions
DNA sequences far from the gene
activators
proteins that bind the enhancer regions to the promoter
control elements
segments of noncoding DNA having particular nucleotide sequences that serve as binding sites for the proteins called transcriptions factors which bind to these elements and reg transcription
Roles of General and Specific Transcription Factors
to initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors
2 types of transcript factors
general and specific
general transcription factors
essential for all protein-coding genes, can also bind to proteins
specific transcription factors
high levels of transcription depending on the interaction of control elements with another set of proteins and this
proximal control elements
located close to the promoter
distal control elements/enhancers
thousands of nucleotides upstream or downstream of a gene or even with an intron, multiple
Transcription Initiation
- Activator proteins bind to distal control elements grouped as an enhancer in the DNA. The enhancer pictured has 3 binding sites, each called a distal control element.
- A DNA-bending protein brings the bound activators closer to the promoter. General transcription proteins and RNA polymerase II are nearby.
- The activators bind to certain mediator proteins and general transcription factors, helping them form an active transcription initiation complex on the promoter.
RNA’s play a role
Small molecules of single-stranded RNA can complex with proteins and influence gene expressions.
2 types of RNAs
small interfering RNAs(siRNAs): another class of small RNAs
- siRNAs and miRNAs are similar but form from different RNA precursors
MicroRNAs(miRNAs): small single-stranded RNA molecules that can bind to complementary mRNA sequences
Both can bind to mRNA and degrade or block its translation.
Zygotes have 3 processes
Cell division, cell differentiation, and morphogenesis
Controls of differentiation morphogenesis
cytoplasmic determinants, cell-cell signals,
Determinism, Pattern formation, Morphogens, Homeotic genes
cytoplasmic determinants
maternal substances in the egg that influence the course of early development, uneven distribution has different results
cell-cell signals
growth factors, produced by one cell influencing neighboring, called induction, causes cells to differentiate
Determinism
aseries of events that lead to the observable differentiation of a cell. Differentiation is caused by cell-cell signals and is irreversible
Pattern formation
sets up body plans. Uses cytoplasmic determinant and inductive signal. Sets up axis (left-right, head-tail, front-back).
Morphogens
substances that play a role with uneven distribution
Homeotic genes
master control genes that control pattern formation.
Oncogenes
are cancer-causing genes
Proto-oncogenes
are genes that code for proteins that are responsible for normal cell growth . Proto-oncogenes become oncogenes when a mutation occurs that causes an increase in the product or an increase in the activity of the protein produced by the proto-oncogene
p53, mitigates cell divisions
- Activate p21 gene –halts cell cycle(CDK), allow for DNA Repair
- Activates a group of miRNAs, inhibit cell cycle
- Directly turns on DNA repair
- Activates “suicide” genes whose products cause apoptosis (cell death)
