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In the absence of tryptophan, E. coli ________ its own tryptophan to survive.
E. coli _______________ its own tryptophan when it is present to _____________ making something that is readily available in the environment
activates a metabolic pathway that makes
stops making
avoid wasting resources
Metabolic pathways can be controlled at the __________ and the __________
Enzyme activity level
Enzyme production level
Metabolic pathway regulation (Enzyme activity)
rapidly adjust the activity of enzymes already present using chemical cues that increase/decrease catalytic activity.
ex): In E. coli, tryptophan (end product) inhibits the first enzyme of the synthesis pathway. This feedback inhibition of anabolic pathways allows cells to adapt to short
Metabolic pathway regulation (Enzyme production)
Cells can adjust the production of enzymes by regulating the expression of genes encoding for them, a longer
It is advantageous to group function
related genes into one transcription unit because
operator
the segment of DNA (within the promoter or between the promoter and the genes) that serves as the "on
operon
made up of the operator, the promoter, and the genes they control when activated, RNA pol can bind and transcribe its genes
Ex): trp operon
repressor
a protein that binds to the operator and blocks the attachment of RNA polymerase to the promoter, preventing transcription. Specific to certain operators on certain operons.
Ex): trp repressor
regulatory gene
a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes. Expressed continuously at low rates.
Ex): trpR codes for the trp repressor
operons are not permanently turned off because
the binding of repressors to operators are reversible
Repressors are allosteric proteins (a molecule must bind/unbind to the allosteric site to change the active/inactive state of the repressor, altering its affinity for an operator)
corepressor
a small molecule that cooperates with a repressor protein to switch an operon off.
ex): tryptophan
repressible operon
an operon whose transcription is usually on, but can be inhibited (repressed) when a specific molecule binds allosterically to a regulatory protein.
Ex): trp operon being inhibited by tryptophan
inducible operon
an operon whose transcription is usually off, but can be stimulated (induced) when a specific molecule binds allosterically to a regulatory protein.
Ex): lac operon is induced by allolactose
beta
galactosidase (enzyme that catalyzes lactose hydrolysis) in E. coli cells
the lac repressor coded for by the lacL regulatory gene is different from the trp repressor because
the lac repressor is active by itself
inducer
a specific molecule that inactivates the repressor.
Ex): allolactose (lactose isomer formed from lactose)
allolactose present = binds to the lac repressor, alters its shape and repressor can't bind to the operator, the lac operon is transcribed, enzymes are made.
no allolactose = lac repressor is active, binds to repressor, and stops gene expression
inducible enzymes
enzymes whose synthesis is induced by a chemical signal
ex): lactose pathway enzymes being induced by allolactose
inducible enzymes usually function in
catabolic pathways, which break down a nutrient to simpler molecules.
cells produce the appropriate enzymes only when the resources are available because
it avoids wasting energy and precursors making proteins that aren't needed.
repressible enzymes
enzymes whose synthesis is inhibited by a chemical signal
ex): enzymes of tryptophan pathway being inhibited by tryptophan
repressible enzymes usually function in
anabolic pathways, which synthesize end products from raw materials.
cells suspend the production of end products when its already present because
the cell can allocate its organic precursors and energy for other uses.
negative control of genes
when operons are switched off by the active form of the repressor protein.
ex): lac and trp operons
gene regulation is said to be positive only when
a regulatory protein interacts directly with the genome to switch transcription on.
E. coli prefers to use glucose over lactose because
the enzymes in glycolysis are continually present. Making enzymes to break down lactose uses energy.
Presence/absence of glucose is detected by interactions with an allosteric regulatory protein and a small organic molecule
Cyclic AMP (cAMP
the small organic molecule that accumulates when glucose is scarce and lactose is present
(inverse relationship w/ glucose)
lactose present, glucose scarce (cAMP high
active CRP)
lactose present, glucose present (cAMP low
deactivated CRP)
activator
a protein that binds to DNA and stimulates transcription of a gene
ex): cAMP receptor protein (CRP)
When active CRP binds to the lac promoter, it _____________ for the lac promoter
increases the affinity of RNA polymerase
(increases the rate of transcription of the lac operon so lac mRNA is synthesized (serves as a transcription factor))
active CRP is an example of positive gene regulation because
it directly stimulates gene expression
If glucose increases
cAMP concentrations fall and CRP detaches from the operon, becoming inactive.
(causes RNA pol to binds less efficiently to the promoter, and transcription of the lac operon proceeds at only a low level (little lac mRNA), even with lactose present)
lac operon is under dual control
Negative control
Differential gene expression
the expression of different genes by cells with the same genome. Causes the differences in cell types/functions, not the presence of different genes.
transcription initiation complexes
On eukaryotic genes, clusters of proteins that assemble on the promoter sequence at the "upstream" end of the gene.
Activators bind to enhancers, and a DNA
RNA polymerase II
transcribes the gene, synthesizing a primary RNA transcript (pre
Control elements
segments that serve as binding sites on eukaryotic genes for proteins called transcription factors.
General transcription factors
acts as the promoter for all genes essential for the expression of all protein
specific transcription factors
binds to control elements away from the promoter
High levels of transcription of particular genes at the appropriate time and place depend on the interaction of control elements and specific TFs
proximal control elements
control elements that are located near the promoter.
enhancer
groups more distant (distal) control elements for a specific gene
It is the __________________, rather than a unique control element, that is important in regulated transcription of the gene.
combination of control elements in an enhancer associated with a gene
Each combo of control elements can activate transcription only when the appropriate activator proteins are present
the appropriate activator proteins are present
In a cell with two different genes, the gene with the correct activators will be expressed while the other missing the activators will not be, depending on the function of the cell
Alternative RNA splicing
regulation at the RNA
Reverse transcriptase
an enzyme isolated from retroviruses that is able to synthesize a complementary DNA copy of an mRNA (reverse transcription)
Each of the fully differentiated cells have a particular mix of
specific activators that turn on the collection of genes whose products are required in the cell
Different sets of activators come to be present in certain cells because
the materials placed into the egg by the mother set up a sequential program of gene regulation that is carried out as cells divide
this program coordinates cell differentiation during embryonic development
The egg's cytoplasm contains both RNA and proteins encoded by
the mother's DNA, which is important genetic info during early development
Cytoplasmic determinants
maternal substances in the egg that influence the course of early development
Induction
the process in which one group of embryonic cells influence the development of another, usually by causing changes in gene expression, done with cell
Master regulatory genes
one or multiple genes that make protein products (transcription factors/activators) that commit cells to becoming a certain type
Apoptosis
programmed cell death. May also occur in mature cells that are infected, damaged, or have reached the end of their functional lifespan
Cellular agents chop up DNA and fragment the organelles and other cytoplasmic components
The cell becomes multilobed (blebbing) and the cell's parts are packaged into vesicles. Scavenger cells engulf the blebs
Apoptosis is triggered by signal transduction pathways, which activates
a cascade of apoptotic "sucide" proteins in the cell destined to die, including enzymes that break down and package blebs
Body plan
an organism's overall 3D arrangement that is established and superimposed on the differentiation process. Allows tissues to function effectively as a whole
Pattern formation
when 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
begins early in the embryo, when the major exes of an animal are established. In bilaterally symmetrical animals, the three major body axes (right/left, front, back) are set up before organs appear
Positional information
the molecular cues that control pattern formation that are provided by cytoplasmic determinants and inductive signals
Cytoplasmic determinants = the mother determines positional info
Homeotic genes
genes discovered by Edward B. Lewis while studying mutated Drosophila that are regulatory genes that control pattern formation
Maternal effect/egg
polarity gene
Bicoid
a maternal effect gene that codes for a protein responsible for specifying the anterior end in Drosophila
Morphogen
a substance that provides positional info in the form of a concentration gradient along an embryonic axis
Ex): bicoid proteins
virus
A tiny, nonliving particle that invades and then reproduces inside a living cell.
Viral genomes may consist of
May consist of double
Capsid
the protein shell enclosing the viral genome
May be rod
Viral envelopes
an accessory structure of influenza and animal viruses that is derived from the membranes of the host cell, containing host cell phospholipids and membrane proteins. Also contains viral glycoproteins and proteins
Bacteriophages (phages)
viruses that infect bacteria
Viral Replicative cycle (Step 1)
The virus enters the cell and is uncoated, releasing viral DNA and capsid proteins
Method of entry depends on virus type (Ex: injection, endocytosis, fusion with plasma membrane)
Viral Replicative cycle (Step 2)
Host enzymes replicate the viral genome
The cell is reprogrammed to help the virus make proteins and replicate the genome, providing nucleotides for viral nucleic acids, enzymes, ribosomes, tRNAs, amino acids, ATP, etc.
DNA viruses use host DNA polymerase along viral DNA templates
RNA viruses use viral RNA polymerase that use RNA as templates.
Viral Replicative cycle (Step 3)
Meanwhile, host enzymes transcribe the viral genome into viral mRNA, which host ribosomes use to make more capsid proteins
Viral Replicative cycle (Step 4)
Viral genomes and capsid proteins self
Lytic cycle
a phage replicative cycle that culminates in death of the host cell in the last stage, when the bacterium lyses (breaks open) and releases the phages that were produced within the cell.
Virulent phage
a phage that replicates only by a lytic cycle
Lytic cycle (step 1)
Attachment
Lytic cycle (step 2)
Entry of phage DNA and degradation of host DNA
Lytic cycle (step 3)
Synthesis of viral genomes and proteins
Lytic cycle (step 4)
Self
Lytic cycle (step 5)
Release
lysogeny
a state in which phage DNA is incorporated into the host cell without lysis
Lysogenic cycle
a phage replicative cycle that allows replication of the phage genome without destroying the host
Temperate phages (𝛌)
phages capable of using both modes of replicating within a bacterium
Prophage
viral DNA that is integrated into the bacterial chromosome.
One prophage gene codes for a protein that prevents transcription of most other prophage genes, making the phage genome mostly silent within the bacterium.
Temperate phage (lytic cycle is induced)
determined by certain factors (environmental, chemical, radiation, etc)
New phage DNA and proteins are synthesized and self
Temperate phage (lysogenic cycle is induced)
determined by certain factors (environmental, chemical, radiation, etc)
Phage DNA integrates into the bacterial chromosome, becoming a prophage
The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells.
Many cell divisions produced a large population of infected bacteria
The infected daughter cells continue living or, occasionally, the prophage will exit the bacterial chromosome, initiating a lytic cycle.
Some prophage genes expressed during lysogeny may alter
the host's phenotype, which can have important medical significance
ex): Three species of bacteria that cause diphtheria, botulism, and scarlet fever wouldn't be so harmful to humans without certain prophage genes that cause the host bacteria to make toxins
Bacterial defenses against phages
Natural selection favors bacterial mutants with surface proteins that are no longer recognized as receptors by particular phages
When phage DNA enters a bacterium, the DNA is often identified as foreign and cut up by restriction enzymes
The CRISPR
Restriction enzyme
enzymes that restrict a phage's ability to replicate within a bacterium by cutting up its DNA
Replicative Cycle of enveloped RNA viruses (step 1)
Glycoproteins on the viral envelope bind to specific receptor molecules on the host cell, promoting viral uptake by the cell
Replicative Cycle of enveloped RNA viruses (step 2)
The capsid and viral genome enter the cell. Digestion of the capsid by cellular enzymes releases the viral genome
Replicative Cycle of enveloped RNA viruses (step 3)
The viral genome functions as a template for synthesis of complementary RNA strands by viral RNA polymerase
Replicative Cycle of enveloped RNA viruses (step 4)
New copies of viral genome RNA are made using the complementary RNA strands as templates
Replicative Cycle of enveloped RNA viruses (step 5)
Complementary RNA strands also function as mRNA, which is translated into both capsid proteins (in the cytosol) and glycoproteins for the viral envelope (in the ER and Golgi apparatus)
Replicative Cycle of enveloped RNA viruses (step 6)
Vesicles transport envelope glycoproteins to the plasma membrane
Replicative Cycle of enveloped RNA viruses (step 7)
A capsid assembles around each viral genome molecule
Replicative Cycle of enveloped RNA viruses (step 8)
Each new virus buds from the cell (similar to exocytosis), its envelope studded with viral glycoproteins embedded in membrane derived from the host cell
Where envelopes are made can depend on the virus
The replicative cycle of animal viruses does not
kill the host cell
Provirus
viral DNA made by retroviruses that enters the host's nucleus and integrates into the DNA of a chromosome and never leaves the host's genome, remaining permanently in the cell.
proviruses are different from prophages because
proPHAGES leave the host's genome at the start of a lytic cycle
replicative cycle of HIV retrovirus (step 1)
The envelope glycoproteins enable the virus to bind to specific receptors on certain white blood cells
replicative cycle of HIV retrovirus (step 2)
The virus fuses with the cell's plasma membrane. The capsid proteins are removed, releasing the viral proteins and RNA
replicative cycle of HIV retrovirus (step 3)
Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to the viral RNA
no proofreading = mutations
replicative cycle of HIV retrovirus (step 4)
Reverse transcriptase catalyzes the synthesis of a second DNA strand complementary to the first
