Chapter 18 - The Genetics Of Bacteria And Viruses Flashcards
What are the two ways that bacteria regulate enzymes?
Feedback inhibition
Operon model
What’s feedback inhibition
Adjusting the ACTIVITY of the enzymes (fast response)
Typical of anabolic pathways
activity of the first enzyme in the pathway is inhibited by the pathways end product –> if tryptophan accumulates in a cell, it shuts down the synthesis of more tryptophan by inhibiting enzyme activity
What’s the operon model?
Regulation of enzyme PRODUCTION (slower)
Catabolic systems
regulate the expression of the genes encoding the enzymes by not transcribing the genes in the first place –> genes encode for the subunits of the enzymes
What are coordinately controlled genes?
5 genes code for the subunits of the enzymes that make tryptophan –> the five genes are clustered together on the bacterial chromosome and a single promotor serves all the genes
The advantage of grouping genes of related function into one transcription unit is that single on/off switch can control the function of all of them
All the enzymes for the metabolic pathway of that amino acid are all synthesized at one time
What is an operator
A segment of DNA that’s the on/off switch for coordinately controlled genes that’s positioned within the promoter or sometimes between the promoter and the enzyme coding genes
What’s a repressor
The trp operon is turned on by itself but the operon can be switched off by the trp repressor which binds to the operator and blocks attachment if RNA polymerase to the promoter to prevent transcription
Since regulatory genes like depressors are always expressed, why isn’t the trp operon switched off permanently
The trp is an also steric protein with two forms
Inky when a tryptophan molecule bunds to the repressor alert an allosteric site does the repressor protein change its shape to the active form which can attach to the operator and turn the operon off
What’s a corepressor?
A small molecule that cooperates with a repressor protein to switch an operon off (tryptophan)
When trp accumulates more trp molecules are associated with the repressor which are then active and bind to operators to shut down pathway enzymes = regulation!
How do bacteria usually respond to environmental change?
Regulate transcription
what are repressible operons?
its transcription is usually on but can be inhibited when a specific small molecule binds allosterically to a regulatory protein
ex. trp operon (need activated repressor to block pathway)
whats an inducible operon?
usually off but can be stimulated when a specific small molecule interacts with a regulatory protein
ex. lac operon:
- regulatory gene, lacI, codes for an allosteric repressor protein that can switch off the lac operon by binding to operator
- the lac repressor is active by itself!
- a special small molecule called an inducer, inactivates the repressor (allolactose)
what are inducible enzyme?
the enzymes of the lactose pathway are inducible enzymes because their synthesis is induced by a chemical signal, allolactose
what is negative control?
regulation of trp and lac operons involves NEGATIVE control of genes because the operons are switched OFF by the ACTIVE form of the repressor
so even though the operon is being turned on in the lac pathway, that’s by the nonactive form of the repressor - the active form of the repressor turns both pathways off
whats an activator?
a protein that binds to DNA and stimulates transcription of gene (CAP) - regulatory protein
cAMP accumulates when glucose is SCARCE and relays to CAP the glucose levels
presence of CAP determines rate of transcription as long as the operon is repressor free
what is positive regulation?
when cAMP binds to the regulatory protein CAP, it assumes its active shape and can attach upstream of lac promoter which increases affinity of RNA polymerase for the promoter
by increasing rate of transcription, the attachment of CAP to the promoter directly stimulates gene expression and is positive regulation!
what is CAP?
an activator of gene expression
glucose low = cAMP –> cAMP + CAP = lac operon ON
glucose high = no cAMP = inactive CAP = lac operon OFF
regulation of chromatin structure
histone acetylation promotes transcription by opening up the chromatin structure!
histone methylation can lead to condensation of chromatin and reduce transcription –> adding a phosphate can help loosen it again
DNA methylation
can methylate certain bases in DNA, usually cytosine
long stretches of inactive DNA are generally more methylated than regions of actively transcribed DNA
what’s genomic imprinting?
methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development
removal of extra methyl groups can turn on some of these genes → once methylated, genes usually stay that way in successive cell divisions
what’s epigenetic inheritance?
inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself
Chromatin modifications don’t entail a change in the DNA sequence
A good reversible mechanism for X-inactivation of regions of genes on one or the other of the two X-chromosomes in human females is enzymatic methylation of histones and/or DNA
what are control elements?
segments of noncoding DNA that are binding sites for proteins called transcription factors
what are transcription factors?
regulate transcription by binding to DNA sites associated w/ controlling activity of a promoter
what are general transcription factors?
some transcription factors are essential for the transcription of all protein-coding genes
a few bind to a DNA sequence like the TATA box within the promoter but most bind to protein like other transcription factors and RNA pol II
what leads to high levels of transcription?
interaction of control elements with another set of proteins called specific transcription factors
what’s an enhancer?
the more distant distal control elements, groupings of which are called enhancers
what are specific transcription factors?
activators or repressors
what strongly effects that rate of gene expression?
The rate of gene expression can be strongly increased or decreased by the binding of either activators or repressors (specific transcription factors) to the control elements of enhancers
DNA bending
Protein-mediated bending of the DNA is thought to bring the bound activators into contact with a group of mediator proteins (they come in separately) which in turn interact with proteins at the promoter
transcription factors that are repressors
can inhibit gene expression by binding directly to control element DNA which blocks activator binding – others interfere with the activator itself so it can’t bind the DNA
what is silencing?
when repressors recruit proteins that remove acetyl groups which decreases gene expression
what’s important in regulating transcription?
each enhancer is composed of 10 control elements, each of which can bind only one or two specific transcription factors – it’s the combination of control elements in an enhancer associated with a gene that is important in regulating transcription of a gene
liver vs. lens cell have different groups of activator proteins
operons and coordinately expressed genes in eukaryotes vs bacteria
co-expressed eukaryotic genes, such as genes coding for the enzymes of a metabolic pathway, are typically scattered over different chromosomes → here, coordinate gene expression depends on the association of a specific combination of control elements with every gene of a dispersed group → activator proteins that recognize the control elements bind to them and promote simultaneous transcription of the genes, no matter where they are in the genome (all have the same colors of control elements which are recognized by a certain activator no matter where they are in the DNA)
different than bacteria where coordinately controlled genes were clustered into an operon which is regulated by a single promoter and transcribed into a single mRNA molecule
what are transcription factories?
Chromosomes in the interphase nucleus aren’t completely isolated
Different loops from the same chromosome or from other chromosomes may congregate in such sites, some of which are rich in RNA polymerases and other transcription associated proteins = transcription factories
how can initiation of translation be blocked?
the initiation of translation can be blocked by regulatory proteins that bind to specific sequences or structure within the untranslated region at the 5’ or 3’ end, preventing the attachment of ribosomes
what is global control?
translation of all the mRNAs in a cell can be regulated simultaneously
usually involves activation or inactivation of one or more of the protein factors required to initiate translation
why can bacteria change their patterns of protein synthesis so quickly?
Bacterial mRNA molecules typically are degraded by enzymes within a few minutes of their synthesis → short life span is why bacteria can change their patterns of protein synthesis so quickly in response to environmental changes
Eukaryote mRNA typically survive for hours, days, weeks
Nucleotide sequences that affect how long an mRNA remains intact are often found in the untranslated region at the 3’ end
how are regulatory proteins activated/inactivated?
by reversible addition of phosphate groups
what is selective degradation?
The length of time each protein functions in a cell is regulated by means of selective degradation → to mark a certain protein for destruction, the cell attaches molecules of a small protein called ubiquitin to the protein → proteasomes recognize ubiquitin-tagged proteins and degrade them
what happens to untranscribed DNA even though 75% of the human genome is expressed at some point?
People used to think the rest of the DNA was untranscribed since it didn’t specify proteins or RNA so therefore it didn’t contain meaningful genetic information → (introns account for only a fraction of this transcribed nontranslated RNA) → this suggests that a lot of the genome may be transcribed into “non-protein-coding RNAs (ncRNA)”
what are two types of small ncRNA?
microRNA (miRNA)
small interfering RNA (siRNA)
what is miRNA? what does it do to mRNA?
Small single stranded RNA molecules capable of binding to complementary sequences in mRNA molecules
miRNA forms a complex with protein and then the miRNA allows the complex to bind to any mRNA molecule with at least 7/8 nucleotides of complementary sequence → miRNA-protein complex then either degrades the target mRNA or blocks its translation
what is siRNA? what does it do to mRNA?
associates with the same proteins as miRNA, producing similar results
the distinction between miRNA and siRNA is based on subtle differences in the structure of their precursors which are both RNA molecules that are mostly double stranded
what is RNA interference?
Blocking of gene expression by siRNA is called RNA interference (RNAi) and it’s used as a means of disabling specific genes
chromatin remodeling by ncRNA
ncRNA can remodel chromatin structure: ex. Formation of heterochromatin at the centromere
what are piwi-interacting RNAa?
they induce formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons
also reestablish appropriate methylation patterns in the genome during gamete formation
evolution of RNA types?
siRNA –> miRNA –> piRNA
what are the stages of zygote development?
1) cell division
2) cell differentiation
3) morphogenesis
what is cell differentiation?
the process by which cells become specialized in structure and function
what is morphogenesis?
the physical processes that given an organism its shape constitute morphogenesis: the development of the form of an organism and its structures
What generates the first differences among cells in an embryo?
The specific genes expressed in any particular cell of a developing organism
what two sources of information “tell” a cell which genes to express at a given time during development?
1) egg’s cytoplasm
2) the environment
what does the egg’s cytoplasm do to tell a cell which genes to express? what are cytoplasmic determinants?
cytoplasm of an unfertilized egg is not homogenous → mRNA, proteins and organelles are distributed unevenly in the unfertilized egg
maternal substances in the egg that influence the course of early development are called “cytoplasmic determinants”
after fertilization, early mitotic divisions distribute the zygote’s cytoplasm into separate cells and the nuclei of these cells can thus be exposed to different cytoplasmic determinants since substances are spread unevenly
what does the environment do to tell a cell which genes to express? what’s induction?
becomes increasingly important as the number of embryonic cells increases
the most influential are the signals impinging on an embryonic cell from other embryonic cells in the vicinity, including contact with cell-surface molecules on neighboring cells and the binding of growth factors secreted by neighboring cells – such signals cause changes in the target cells, a process called induction – the molecules conveying these signals within target cell are cell-surface receptors and other signaling pathway proteins
signaling molecules send a cell down a specific developmental path by causing changes in its gene expression that eventually result in observable cellular changes
what is determination?
a term that refers to the point at which an embryonic cell is irreversibly committed to becoming a particular cell type – once it undergoes determination, it can be placed in another location in the embryo and still differentiate into the cell type that is its normal fate
what are determined muscle cells called?
myoblasts
what is a master regulatory gene?
Researches identified several “master regulatory genes” whose protein products commit the cells to becoming skeletal muscle → the molecular basis of determination is thus the expression of one or more of these master regulatory genes
how does determination work?
signals from other cells lead to activation of master regulatory gene, myoD, –> cell then transcribes mRNA and makes myoD protein (a transcription factor that acts as activator)
the cell is now a myoblast and is committed to being muscle cell
how does differentiation work?
myoD protein stimulates myoD gene further to make more myoD –> myoD then activates other genes that are necessary to make the cell a muscle cell
also turns on genes that stop cell cycle division of nondividing myoblasts fuse to become mature muscle cells/fibers
what is pattern formation?
Cytoplasmic determinants and inductive signals both contribute to the development of a spatial organization in which the tissues and organs of an organism are all in their characteristic places
what is positional information?
o The molecular cues that control pattern formation are collectively called positional information and are provided by cytoplasmic determinants and inductive signals
These cues tell a cell its location relative to the body axes and to neighboring cells
what’s modular construction?
an ordered series of segments – the segments make up the body’s three major parts:
- head
- thorax
- abdomen
fruit flies and anthropoids have this
what are homeotic genes?
control pattern formation in the late embryo, larva, and adult
what are embryonic lethals?
mutations with phenotypes causing death at the embryonic or larval stage → since these organisms never reproduce, they can’t be bred for study
Mutations affecting a process as fundamental as segmentations would surely be embryonic lethals
what play a role in axis formation in drosophila?
cytoplasmic determinants –> they would also have to look at DNA of mom to identify all the genes that affect segment formation
how did researchers determine which genes effected segment formation?
mated mutagenized flies then scanned their descendants for dead embryos or larvae with abnormal segmentation/defects
ex. To find genes that might set up the anterior-posterior axis they look for embryos/larvae with abnormal ends like two heads/tails and predict that such abnormalities would arise from mutations in maternal genes required for correctly setting up the offspring head
what are maternal effect genes?
Cytoplasmic determinants establish axes of Drosophila body → these substances are encoded by genes of the mother called maternal effect genes: a gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring’s own genotype!
also called egg-polarity genes
what is bicoid? whats the morphogen gradient hypothesis?
a morphogen that determines head structures –> mom that has two mutant bicoid alleles lacks the front half of its body
example of the morphogen gradient hypothesis where gradients of substances called morphogens establish am embryo’s axes and other features of its form
what are oncogenes?
cancer-causing genes which are carried in certain types of viruses (counterparts were found in animals)
oncogenes arise from genetic change that leads to an increase either in the amount of the proto-oncogene’s protein product or in the intrinsic activity of each protein molecule
what are photo-oncogenes?
normal version of the cellular genes that code for proteins that stimulate normal cell growth and division
what are the three changes that convert photo-oncogenes to oncogenes?
1) movement of DNA within genome - if it ends up near active promoter transcription may increase
2) amplification of proto-oncogenes: increases # of copies of gene through gene duplication
3) point mutations in a control element which causes increase in gene expression or produce a more active protein
what are tumor suppressing genes?
genes whose products inhibit cell division because the proteins they encode help prevent uncontrolled cell growth
repair damaged DNA which prevents the cell from accumulating cancer-causing mutations, control adhesion of cells to each other, other proteins are components of cell-signaling pathways that inhibit the cell cycle
ras gene? mutations?
ras gene is a porto-oncogene that relays signals from growth factors to a cascade of protein kinases and the response is stimulation of cell cycle
pathway won’t operate unless triggered by appropriate growth factor but certain mutations in as gene can lead to production of hyperactive as protein that triggers kinase cascade even in absence of the growth factor being bound to the receptor
p53? mutations?
sometimes when there’s damaged DNA, an intracellular signal leads to synthesis of a protein that suppresses the cell cycle
the genes for the components of these pathways act as tumor-suppressor genes (p53) - it encodes a specific transcription factor that promotes synthesis of protein that inhibits cell cycle
so…a mutation that knocks out the p53 gene can lead to excessive cell growth and cancer
what mutations are common in individuals with colorectal cancer?
Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer
what is heterogeneity?
tumors differ in significant ways! that’s what makes curing cancer so hard
