BSCI331 Exam 3

most common way a cell can receive signals

cell surface receptor

3 phases of cell reception

1. Reception: binding of ligand to cell surface receptor

2. Transduction: transfer of information from inside to outside (usually has a signal pathway)

3. Cellular response

In most cases how are signal molecules created?

they are secreted — released from one cell and diffuses to reach another cell

Secreted molecules that travel locally, affecting cells in the immediate environment is called?

paracrine signals

secreted molecules that act over long distances through the bloodstream?

endocrine signaling

secreted molecules that travel through axons

synaptic signaling — specific and knows who the receptor is, unlike endocrine and paracrine signaling

paracrine signaling graphic

paracrine signaling graphic

synaptic signaling graphic

can cells secrete a molecule that binds to its own receptor

yes — autocrine signaling

why would we ever have autocrine signaling cells?

Cells are autocrine to self-stimulate, allowing a single cell to regulate its own growth, survival, and differentiation by releasing signaling molecules that bind back to its own receptors. Having this provides instant feedback for rapid responses, immune cell activation (e.g., T-cells), and tissue

why would a signaling molecule stay on the surface?

contact dependent signaling and this happens in vital developments such as embryonic development to ensures precise localized signaling of the moelcule in the active site

Extracellular molecule signalling can work in 2 ways

Rapid or slow

how does rapid extracellular molecule signalling work

it immediately alters the proteins function which then alters the cells behavior

how does slow extracellular molecule signalling work

the extracellular molecule does not immediately alter the protein function, but it send a cascading message inside the nucleus and then goes DNA —> RNA and synthesizes the protein and then alters the cells behavior

causes transcription and the expression of new genes

Rapid and Slow extracellular signalling graphic

how do multiple signal receptors on a cell work?

they all must superscore for a specific response —> alters the protein function —> changes cell behavior

can multicellular organisms decide to die on its own?

no

what is one way in which a cell is destined to survive

receiving the necessary cells to “tell it” to survive, missing these results in deahth

what is the name of the suicide cells commit when they dont receive the necessary signals?

apoptosis

are each survival signalds restricted to the specific environment in the body?

yes

can different receptors bind to the same transport moelcule (ligand)

yes, cardiac cells, mouth cells and skeletal muscle cells all have different receptors that bind to Ach and cause different outcomes — due to different internal machinery

can the same signaling molecule cause different protein alterations and cell responses based on it’s concentration?

yes

cells are specialized to receive and respond to a wide variety of stimuli

• mechanical: cells can tell they are in contact with something else when the internal machinery is distorted, detect pressure such as being smushed, sound from people

• light: nerves from retina where we can see

• heat: feel the fire from the other day

• chemical: amino acid signals, nucleotides, small peptides, proteins, steroids, fatty acids, gases, hormones all binding to receptors

  • Most of these cells are created through exocytosis and secreted

Lipid soluble molecules

signaling molecule that diffuses past the plasma membrane

• steroid hormones, cortsol, sex horomones, vitamin D

how do the hydrophic molecules travel to their receptors

lipid soluble/NP signals bind to carrier proteins and bind to their respective intracellular receptors which be cystolic of nuclear

what are the family of intracellular receptors that bind to llipid soluble singnals?

nuclear receptor subfamily

what state is the nuclear receptors in before the ligand binds?

inactive — bound to an inhibitory protein

• contains a ligand binding, DNA binding and tracription activating domain

when the ligand binds to the nuclear receptor what happens?

It causes a conformational change and releases the nuclear receptor from the inhibitory protein, allowing it to fold into its correct shape and travel to the DNA, causing transcription

• It can bind directly to RNA polymerase or chromatin remodeling (loosens) and activates transcription

what is great about NP/lipid soluble signal molecules?

the receptors are also the downstream molecule

• no need of an additional pathway making it fast

what are the majority of the signal molecules?

hydrophilic/lipid insoluble signals

• neurotransmitters, peptides, GF, olfactants and tastants

what type of receptors are present for insoluble/polar molecules?

cell-surface receptor proteins that bind to hydrophillic signal moelcules

what are the three main types of cell-surface receptors?

1. ion-gated channels

2. enzyme-coupled receptors

3. G-protein coupled receptors

how do ion gated channels work?

a protein forms a channel which is closed, when the ligand binds, it opens the protein channel allowing ions to flow across the channel

how does enzyme coupled receptors work?

signal molecule binds to the protein receptor, allowing it to form a conformation where the inactive kinase receptor dimerizes allowing one to phosphorylate the other and VV increases the activity of the kinase and phosphorylates the signaling

Keep in mind enzyme-coupled receptors can also work by having the kinase domain act as a separate protein that is tightly associated with the receptor (non receptor tyrosine kinases)

how do G-protein coupled receptors work?

signal molecule binds to the receptor, shifting the G-protein complex over allowing the G-protein to release GDP and bind GTP, putting it in the active state. The alpha chain seperates from the beta and gamma chains, allowing the alpha chain to bind to other enzymes

are extracellular receptors the same as the one-and-done nuclear receptors that act as the downstream effect

NO

what do we use to send the signal in the extracellular signaling proteins?

intracellular signaling proteins that lead to protein alteration and change in cells activity

what do the secondary messengers do?

amplify the signal and spread it throughout the cell

what benefit do signal transduction pathways have over nuclear receptor paths

branch and amplify the signal

many intracellular signaling proteins function as what?

switches — kinases and phosphates
(phosphorylation and dephosphorylation)

what are signaling complexes

They are when multiple proteins assemble together inside cells to rapidly transmit external signals from receptors to intracellular targets

• speed

• efficient

• specific

what are some ways we can assemble intracellular protein signaling complexes

1. scaffold protein vertically

2. receptor serves as it’s own scaffold

3. membrane lipids act as the scaffold

scaffold protein vertically

non enzymatic proteins that act as an adaptor and keep intracellular signaling proteins organized

receptor serves as it’s own scaffold

the cytoplasmic portion of the receptor serves as bidning sites for the intracellular signaling proteins

membrane lipids act as the scaffold

When a ligand binds a receptor tyrosine kinase, the receptor becomes activated and recruits enzymes such as PI3K that phosphorylate membrane phosphoinositides. These phosphorylated lipids serve as docking sites for cytoplasmic signaling proteins, allowing them to assemble at the membrane and generate downstream signaling. Lipid rafts help concentrate receptors and phosphoinositides to make this process more efficient.

receptor tyrosine kinase activation

Inactive RTKs bind a ligand, which causes dimerization. This brings the kinase domains together, allowing them to activate and cross-phosphorylate each other on tyrosine residues.

what makes RTKs (receptor tyrosine kinases) so damn special

they allow the docking of intracellular singaling proteins to the phosphorylated tyrosines via SH2 domains forming a signaling complex downstream amplifying the lignad binding ti the RTK

Graphic of RTK

ligand binds to the RTK allowing the receptor to dimerize and phosphorylate resulting in intracellular binding proteins binding to the docking sites on the phosphorylated Tyrosines via SH2 domain

after RTK is phosphorylated what can the signal be passed to?

Ras

what does Ras do?

it causes a kinase cascade

what type of protein is RAS?

it is a G-protein which is activated when GTP is bound

order of RTK and Ras

1. RTK gets phosphorylated

2. Ras becomes activated (GTP on)

3. Ras activated a cascade: Raf, Mek, Erk (each step gets phosphorylated via MAP kinase)

4. Erk activated proteins and causes transcriptional factors

graphic of G-protein coupled receptor

G-protein is activated, causing GDP → GTP swapping, allowing the alpha unit to break off and bind to other enzymes and regulating their function

G-protein stimulated adenylyl cyclase, converting ATP to cAMP, a secondary messenger bind and bind to the cAMP responsive protein kinase A where it can diffuse in the cytosol or nucleus

A graphic of protein kinase A diffusing in the nucleus and activating CREB, where it binds to CBP and leads to gene transcription

does the alpha subunit in the G-proteins vary

Yes, they can bind to adenylyl cyclase or any other enzyme causing different behaviors

What is the storyline of G-protein receptors?

Bind → GDP→GTP → split alpha subunit → activate enzyme → make second messenger → response → GTP hydrolysis off

what is the role of Ca2+ ions in intracellular communication

they are second messengers

what activities do Ca2+ ions have a role in?

muscle contraction, cell division, secretion, synaptic transmission

Graphic of gene expression regulation and what points along central dogma we have checkpointst

What is the first point of gene regulation?

transcriptional control

for most genes where does the primary regulation occur?

RNA transcription

how can we maximize the central dogma?

create only the amount of RNA we need to transcribe into protein so we don’t waste ATP

where is the location of regulating RNA transcription?

initiation

what are the things that regulate transcription called?

transcription factors

what is the special structure of the transcription factor that aids in regulation

DNA-binding motifs

what do DNA-binding motifs do

they find and bind to specific nucleotide sequences in the DNA through the grooves and increase/decrease RNA polymerase activity

why do transcription factors prefer the major groove?

they bind to the major groove because it exposes more information about the DNA

How does the formation of transcription factors bind to the DNA

the DNA-binding motifs have H-bond acceptors which bind to the H-bond donors of teh base sequences of DNA to create that “lock” and alter RNA polymerase activity

How many DNA-binding motifs are there?

6 different DNA-biding motifs

Helix-turn-helix DNA-binding motif

2 alpha-helices which are conncected by a short unstructured turn with the c-terminus recognition helix makes contact with the major groove of DNA

Homeodomain DNA-binding motif

3 alpha turn helices which create bonds with the major groove on the c-terrminus and bonds with the minor groove in the n-terminus

Zinc fingers DNA-binding motif

consisted of an alpha helix and a beta sheet, where the alpha helix binds to the major groove of the DNA while it is stabilized by the Zinc ion

We can alter the specific sequence of amino acids in the alpha helix to create whatever recognition we want

Zinc fingers DNA-binding motif (second one!)

This zinc finger model has 2 Zn ions, one is used in the middle of the motif like normal, and the other one is used to stabilize a loop involved in creating DIMERIZATION which bind to DNA as symmetric dimers

Leucine zipper DNA-binding motif

2 Alpha helices formed dimerized together, with the C-terminus having NP bonds such as Leucine forming a zipper and the other end having Polar bonds (N-terminus) making bonds with the DNA

DIMER

Helix-loop-helix DNA-binding motif

2 alpha helices are held together — one short alpha helix and another long alpha helix held together by a flexible loop

DIMER

Why do we have these DNA-binding motifs that bind in the major groove using their alpha helices as dimers?

We use dimerized DNA-binding motifs such as leucine zippers, zinc fingers, and helix-loop-helix to enhance the binding and specificity to double the contact area and square the affinity

what are the benefits of heterodimerizing?

increase the range of sequences that can be recognized

How many different sequences can be recognized by a dimerization of a TF with A, B and C

AA, AB, AC, BC, CC, BB

*AC and CA are the same and result in the same transcription response so that doesn’t count”

Where do transcription factors usually act on in initiation?

Promoters and Enhancers

What is the promotor

Region of the DNA where the RNA polymerase and general transcription factors (essential enzymes used to aid the RNA polymerase in binding to the promoter) assemble

where is the promotor located

just upstream of the 5’ end

can promotors be gene-specific?

yes, they can which means they only work when they are located to their adjacent gene and orientated right

What is an enhancer

independent region outside the promotor which can be very far away which can boost the transcription of a specific gene

why do TFs bind to the enhancer and promoters

they are both used in either aiding in transcription or initiating it

can enhancer work with other promotors? (coworkers)

yes with a heterologous promoter

How can we use the TF to modify the transcription and thus the gene expression?

The TF factors can bind synergistically or antagonistically producing different effects

what is going on here?

the TF are binding to the enhancers and regulatory sequences very close to the promotor, then the mediator protein causes the DNA to loop allowing the TF to interact with the promotor region

what does the lac operon do?

it creates structural enzymes to bring in and break down lactose when it is available in the environment

how does the lac operon work in the differing environments?

No Lactose: there is no point in running ts so the Lac I regulatory sequence has an active repressor bind to the promotor to prevent RNA Poly from transcribing the gene to make the lactose destroyers

Lactose Present: lactose converts to allolactose allowing it to act as an inducer binding to the repressor moving it away

When we have Low Glucose: we bind a CAP which carries cAMP to the CAP binding site, now keep in mind if lactose is low we still have the repressor but if lactose levels are high and glucose levels are low we will have the CAP/cAMP as well as the repressor not being bound so there is transcription

what mechanisms do TF actually regulate after they bind to regulatory sequences such as promoters and enhancers?

1. help unpack chromatin making the gene more accessible for RNA polymerase promoting transcription

2. help recruit more GTF by binding close to the promoter

3. can regulate the switch from initiation to elongation

4. recruit histone-modifying enzymes to change the local chromatin structure

5. can bend the DNA allowing long-distance TF to interact between regulatory sequences

how do we regulate TF?

we can’t have all of the TF on all at once or else there’s no regulation

they’re pretty smart, they bind when they are needed and don’t when they aren’t needed

• some TF are for tissue specific expression — TF only bind to liver when needed

• some TF are only expressed based on environmental signals — like hunger

• some TF are made only during some phases of the cell cycle

why are some TF incactive in the cells?

so the cell can regulate when we want to turn genes on

how can we activate TF

signaling pathways such as RTKs (MAPK occurs downstream), or the kinase enzyme phosphorylating the TF

What is NFAT and NF-κB

they are both TF that are inactive in the cytoplasm until the genes are told to turn it on

NFAT process (triggered by T cells)

inactive TF in the cytoplasm that is phosphorylated, when Ca2+ increases it activates a phosphatase that dephosphorylates the NFAT and allows it to move into the Nucelus to activate genes

NF-κB process (triggered by T cells)

NF-κB is bound to an iκB inhibitor, when iκB is phosphorylated it becomes ubiquinitized and degreades allowing the NF-κB to move into the cell and result in gene transcription

how is it regulated? NEGATIVE feedback loop: newly synthesized IκB inhibits NF-κB and returns it to the cytoplasm

what is the combinational control of gene expression?

Combinatorial control of TF produces spatial patterns of gene expression, such as the striped expression of the even-skipped gene in embryos

how do we get this on/off sequence of one gene?

what we are used to which is a gradient of TF in the DNA, this is not that case and actually it requires enhancers

how can we express only one of the stripes on it’s own?

Each stripe is controlled by its own enhancer module that integrates inputs from multiple transcription factors to produce expression in a specific region.