BIOS 3450 Post Exam 2

ligand

signaling molecule, binds to receptor

signaling

proteins and second messengers are __ molecules

amplification

binding of signlaing molecules to receptors ___ of signals via downstream processes

downstream process

binding of signaling molecules to receptors amplififcation of signals via ____

contact-dependent

a type of cell signaling requiring a membrane bound signal molecule on a signaling cell binding to a receptor on a target cell (cells are “touching”)

paracrine

a type of cell signaling where 1 cell secretes a molecule (local mediator) that acts on a second cell in close proximity

synaptic

a type of cell signaling that only occurs in neurons, where signal molecules (neurotransmitters) are sent from one nerve cell across the synapse (junction between nerve cells)

endocrine

a type of cell signaling where signal molecules (hormones) are sent to target cells far way via the bloodstream

gap junction signaling

a type of cell signaling where signal molecules are sent from a signaling cell to a target cell via gap junctions that connect the cells

autocrine

a type of cell signaling where the cell targets itself

autocrine

IL1 cytokines produced by monocytes binding to receptors on monocytes is an example of ___ signaling

gap junction

muscle cells sending Ca2+ through gap junctions to other muscle cells is an example of ____ signaling

quorum sensing

how bacteria determine if they have enough numbers to do certain things

high

bacteria’s Al synthase (Lux1) binds to the Lux R receptor leading to the expression of luciferase genes when bacteria are in ___ density

steroids

example of intracellular signal molecules

intracellular receptors

receptors taht are located inside of the cell

survive, grow + divide, differentiate, die

the options of pathways for cell signaling to cause

GPCRs, ICCR, ECRs

types of cell-surface receptors

serine/threonine kinases, tyrosine kinase

the two kinds of intracellular signaling molecules that cell surface receptors relay signals to

GTPase activating protein

negative regulator of GTPase, promotes conversion of active GTPAse-GTP to inactive GTPase-GDP

histadine kindases

intracellular signal molecules in bacteria

G-Protein coupled receptors (GPCRs)

proteins located on the cell surface that recognize extracellular substances and transmit signals across the cell membrane by activating guanine nucleotide-binding proteins (G protein) that are responsible for signal transduction inside the cell.

ion channel coupled receptors (ICCRs)

proteins comprised of a G protein-coupled receptor and a fused ion channel, engineered to couple channel gating to ligand binding

enzyme coupled receptors (ECRs)

a type of single-pass transmembrane protein that contains a ligand-binding site outside the cell and a catalytic unit inside the cell

conformation

ligands binding to receptors result in change in ____

alpha and gamma

proteins in G-protein complex that are membrane anchored

heterodimer

dimer made of two different proteins

homodimer

dimer made of two of the same proteins

adenylyl cyclase

enzymes that catalyze the production of cyclic adenosine monophosphate (cAMP) from adenosine triphosphate (ATP).

cyclic AMP (cAMP)

many GPCRs activate adenylyl cyclase leading to increased ___ productionc

calcium (Ca)

universal eurkaryotic intracellular messenger

activated PKC

controls cellular processes by phosphorylating target proteins to regulate cell proliferation, differentiation, apoptosis, and gene expression + migration

vision and olfaction systems

use GPCRs regulating c-GMP gated ion channels

vision systems

light —> activate G-proteins —> GMP phosphodiesterase activated —> GMP hydrolized —> cation channels close —> altered membrain potential —> brain signal

receptor tyrosine kinases (RTKs)

major class of ECRs

Ras

crucial genetic switch in many growth factor signaling pathways

RTKs, GPCRs

two receptor complexes that can activate overlapping signaling pathways with each other

primary culture

cells taken directly from an organism

cell line

cells that can be cultured indefinitely in vitro

fractionation

used to open up cells to get organelles

french press, sonicator

used to break open cells gently during fractionation, keeps organells in tact

glucose gradient, centrifuge

used to isolate organelles after splitting open cells

column chromatography

used to purify proteins

charge, size, affinity

ways to sort proteins during column chromatography

ion exchange chromatography

chromatography used to sort proteins by charge

gel-filtration chromatography

chromatography used to sort proteins by size

affinity chromatography

chromatography used to sort proteins by affinity to added reagent

primary cultures

require attachment, senescence after limited number of cell division, contact inhibited (grow as monolayers on culture dishes), differentiated cell types may require 3D structure support or “feeder” layer of cells

transformed (stem) cell lines

can grow in liquid suspension, can be cultured indefinitely, not contact-inhibited, form 3D mounds or balls, relatively undifferentiated

SDS (sodiumdodecyl sulfate)

detergent that denatures proteins and coats them with a negative cahrge

southern blot

gel electrophoresis used for sorting DNA treated with restriction enzyme by size

northern blot

gel electropheresis used for sorting single-stranded RNA by size

western blot

gel electrophoresis used to sort denatured proteins by size (happens after SDS PAGE)

immunoprecipitation

used to isolate proteins or specific cell types, a technique in which an antigen is isolated by binding to a specific antibody attached to a sedimentable matrix

mass spectrometry

used to separate ionized samples based on their mass-to-charge ratio and measuring their relative abundance

X-ray crystallography

determines the 3D atomic and molecular structure of crystalline proteins

PCR (polymerase chain reaction)

a laboratory technique for rapidly producing (amplifying) millions to billions of copies of a specific segment of DNA

Taq polymerase

used as DNA polymerase in PCR to synthesize DNA strands

gel electrophoresis (agarose)

used to separate DNA by size (not denatured with SDS)

recombinant DNA

a gene of interest is cloned and “pasted” into plasmid cleaved with restriction enzyme

reverse trasncriptase

an enzyme that converts RNA into DNA, used for making cDNA libraries

cDNA library

a collection of cloned DNA copies derived from the messenger RNAs (mRNAs) of a specific cell type at a particular time

sanger sequencing

a fast, cost-effective way of reading the sequence of small targeted regions of the genome.

sanger, shotgun, high throughput, pyro

DNA sequencing methods

shotgun, high throughput, pyro

computational DNA sequencing methods

in situ hybridization

use labeled single-stranded DNA or RNA that binds to a complimentary sequences inside of fixed, dead cells to localize a sequence of DNA or RNA

CHIIP

used to look at hte genetic strucutre of DNA, shows DNA-protein interactions

RNA seq

quantifies RNA molecules in a sample, a method for sequencing an entire set of RNA molecules. This method involves isolating RNA molecules in the tissue or cell sample, copying those RNAs into DNA and then sequencing the resulting DNA molecules.

up regulated

toward the right of a volcano plot

down regulated

toward the left of a volcano plot

increased up regulation (significant change in regulation)

toward the top of a volcano plot

ish regulation (insignificant change in regulation)

grey points on volcano plot

DAPI

blue stain used to visualize nucleus

low energy wave

wave with long wavelength and low frequency

high energy wave

wave with short wavelength and high frequency

white light microsocopy

microscope that uses visible light to illuminate and image a specimen

bright field, dark filed, phase contrast(DIC)

types of white light microscopy

inverted microscope

type of microscope used for white light microsocpy on cells in culture dish

microtonne

used to slice tissue to make microscope slide specimens

cryostat

used to slice frozen tissue to make microsocope slide specimens

electron microscopy

electron beams interact with fixed specimen, higher resolution than brightfield

scanning electron microscopy (SEM)

electron beam scans teh surface of specimen, creates 3D sample

transmission electron microscopy (TEM)

electron beam passes directly through specimen, creates an image that reveals the internal structure and organization of the specimen

cryo electron microscopy (cryoEM)

specimen flash frozen in water, uses TEM to create image taht allows proteins and viruses to be visualized “as they exist in real life”, used for TM proteins

immunofluorescence

specific proteins are tagged so they can be seen under a microscope, proteins tagged with secondary antibodies that have fluorescent marker on them

antigen

antibody can be generated against

epitope

exact structure that an antibody recognizes

fluorescent molecules

absorb light when excited at one specific wavelength and emit it at another longer wavelength

fusion protein

fluorescent protein bound to a protein of interest

fluorescence resonance energy transfer (FRET)

tracks interactions between molecules in real time, when two tagged proteins interact they emit a specific light/signal

flow cytometry

allows detection of fluorescent molecules inside a cell, a technology that rapidly analyzes single cells or particles as they flow past single or multiple lasers while suspended in a buffered salt-based solution

actin, microtubels, intermediate filaments

cytoskeleton components

chemoattractants

what neutrophils use to direct movement to specific targets

rapid cytoskeletal rearragnements

allow neutrophils to puruse bacteria

formyl peptide receptors (FRPs)

allow neutrophils to detect bacterial N-formyl peptides

self-assembling subunits

cytoskeleton components are organized polarized epithelial cells made of _____

globular actin (G-actin)

type of actin, binds to ATP —> ATP slowly hydrolizes as it moves along the filament

treadmilling

the process of F-actin polymerizing at the + end and depolymerizing at the - end, which can lead to filament translocation

actin polymerization

ATP bound monomers attach to + end of the filament and ADP bound monomers detach from - end