Gene Regulation

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 __________

1. Enzyme activity level

2. 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

1. the binding of repressors to operators are reversible

2. 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)

1. New phage DNA and proteins are synthesized and self

Temperate phage (lysogenic cycle is induced)

determined by certain factors (environmental, chemical, radiation, etc)

1. Phage DNA integrates into the bacterial chromosome, becoming a prophage

2. The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells.

3. Many cell divisions produced a large population of infected bacteria

4. 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

1. Natural selection favors bacterial mutants with surface proteins that are no longer recognized as receptors by particular phages

2. When phage DNA enters a bacterium, the DNA is often identified as foreign and cut up by restriction enzymes

3. 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