Cell bio vocab | Course Paper

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Aug – the 3 letter start codon

Glutamic acid – an example of a (-) polar amino acid

paralog – homologous genes that are within one genome

disease – protiens that assist folding

miRNA – type is small RNA that requires Dicer for it generation

tRNA synthetase – enzyme that covalently attaches an amino acid to its tRNA

s bombe – a single celled fission yeast used for cell cycle studies

genome – complete set of DNA

phosphatase – enzyme that catalyzes dephosphorylating of a protein

activation energy – free energy required to reach a substrates transition state

phosphorylation – an example of post translational modification

van der Waals – weakest non covalent bond

barrier – sequence that blocks the spread of heterochromatin

transcription bubble – region of unpaired DNA exposed by RNA polymerase

flippase / scramblase – Enzyme that moves lipids across membrane leaflets

trans SNARE complex – Four-helical protein bundle required for vesicle fusion

autophagy – “Self–eating” of cytosol and organelles at the lysosome

trans – Golgi “face” from which vesicles depart

dynein – Minus end directed microtubule motor protein

ran – GTPase that regulates nucleocytoplasmic transport

endocrine – Cell2cell signaling that occurs over long distances

lipid raft – Thick, cholesterol-enriched domain within a lipid bilayer

multivesicular body – Endosomal compartment with many intraluminal vesicles

Golgi/er – Organelle where sugar modifications typically occur

signal peptidase – Enzyme that cleaves a signal sequence

arp2/3 complex – Actin nucleator that generates branched F-actin networks

FRAP – Photo bleaching method that quantifies protein mobility

(+) plus end – Fastest growing end of F-actin

active transport – Transport against an electrochemical gradient:

19s caps – part of the proteasome that unfolds incoming polypeptides

DNA helicase – unwinds dna double helix during replication

Brenner – Nobel prize for the studies on programmed cell death

cdc25 –phosphatase that removes an inhibitory phosphate on CDK

lysosome – acidic organelle that can digest protein aggregates

telophase –stage of mitosis when the nuclear envelope reassembles

mitochondria pathway – apoptosis pathway that is regulated by cytochrome C

transition – check point after which a cell commits to cell cycle entry

pexophagy autophagy destruction of peroxisomes

s phase- cell cycle phase in which most histone synthesis occurs

deurinetia – mutation ultimately resulting in deletion of nucleotide pair

astol – microtubules who’s plus ends interact with the cell cortex

mitophagy 0 type pf autophagy that does not involve an auto phagosome

Apart 1 – adaptor protein within apoptosome.

light microscopy – uses visible light to detect small objects. light microscope has a limit of

resolution (~200 nm) that depends on the wavelength of light … objects <200 nm cannot be easily

resolved

electron microscopy- uses a beam, of electrons to create an image of a specimen

limit of resolution-

wavelength of light

super resolution microscopy – an increase the resolution of conventional light microscopy (down

to 20 nm)

condenser-

objective-

lenses – in the condenser focus light on the specimen

dark field microscopy- see a dark field with a bright object. works because oblique rays of light

that don’t enter the specimen aren’t directed to the objective; only light that is scattered by parts

of the cell will inter the objective

phase contrast microscopy- built of a fundamental principle: the “phase” of the light will change

as it passes through a cell

refractive index-

fluorescence microscopy- can be used to visualize different parts of cells or molecules

photon

fluorophore- fluorescent chemical compound that can re-emit light upon light excitation

1st filter set- selects for excitation light

2nd filter set- selects for emission light

Aequorea Victoria- jelly fish known for its naturally occurring green fluorescence around the ring

of its bell, in large thanks to the presence of 2 fluorescent protein: Aequorin and GFP

Aequorin- protein that emits blue light when bound by calcium

Green Fluorescent Protein –

Osamu Shimomura, Martin Chalfie, and Roger Tsien- Nobel prize in chemistry for the discovery

and development of the GFP

FRAP- fluorescence recover after photo bleaching

FRET- fluorescence resonance energy transfer

photo activation- use a caged fluorophore which is activated locally upon a strong pulse of light

airy disc

PALM-

STORM-

immunogold labeling-can be used to get high res localization data w EM

cryoEM-

single-particle reconstruction-

track the expression of a gene- tell when and where a promoter is active

track organelles- just attach the GFP coding sequence to a sequence that codes for a specific

localization signal

track proteins- just need to put GFP sequence downstream (or upstream) of a gene of interest.

produces a chimeric protein

measure protein mobility- use fluorophore- protein fusions, and a perform fluorescence recovery

after photo bleaching (FRAP)

monitor protein protein interactions- use fluorophore protein fusions, and perform florescence

resonance energy transfer (FRET)

photo activation- use a “caged” fluorophore which is only activation locally upon a strong pulse of

light

transgenic animal- animal that has been genetically engineered by gene deletion or gene

replacement

transgene- foreign or modified gene that is added

double stranded breaks- Remember: typically, double strand breaks are bad and need to be

repaired. But, experimentally, scientists can make double strand breaks and use natural “repair”

machinery to then remove or insert sequences.

CRISPR- clustered regularly interspaced short palindromic repeats

Cas9- endonuclease the dual rna complexes binds to; The Cas9 enzyme then cuts the viral double

stranded DNA, rendering it inactive

guide RNA- Guide RNA AKA sgRNA (this is essentially a crRNA/tracrRNA fusion); the guide RNA

sequence complementary to the genome is what gives specificity

Charpentier and Doudna- 2015: Charpentier and Doudna win the Breakthrough Prize in Life

Sciences

Breakthrough Prize in Life Sciences- 2015: Charpentier and Doudna win the Breakthrough Prize in

Life Sciences

CRISPR loci – can have several hundred repeats interspersed with sequences from previous viral

infection (most recent at the 5’ end, so provides a temporal history)

repeat sequence –

pre crRNA- The full locus is transcribed as one pre-crRNA

crRNA – detect viral DNA upon subsequent exposure, and bind via complementarity

tracRNAs- The transcript is subsequently bound by other RNAs known as tracrRNAs (bind to the

repeat sequences), which allow processing into individual crRNAs

PAM sequence- PAM sequence must also be present (protective role in bacteria, because not

present in the actual CRISPR loci, just viral DNA targets; so it can distinguish its own genome from

the virus)

5’-NGG-3’– is the consensus for the PAM site

INDEL- Insertion or deletion (INDELS) of 1 or 2 bases creates a frame-shift

“first to file”–

CRISPRa- express an inactivated Cas9 enzyme fused to a transcriptional activator or RNA pol II. a

stands for activation

CRISPRi- CRISPRi: express an inactivated Cas9 enzyme fused to a transcriptional repressor. I

stands for inhibition

deamination- Remember, spontaneous deamination of C to U can bring about permanent

changes to the DNA sequence …

cytidine deaminase- which catalytically changes C to U (within ~5 nt of the region of

complementarity defined by the sgRNA)

Cas13- an RNA guided RNase

recreational gene editing- as in “designer babies” (not yet, but now a very real possibility)

gene drives- mechanisms that defy the laws of inheritance. By forcing inheritance of a certain

trait, these have the potential to disrupt the natural evolution of a species.

cancer-

neoplasm

tumors- cancers will form neoplasms (neo or new growths)

benign tumor- one in which neoplasmic cells have yet to become invasive

malignant tumor- one in which neoplasmic cells have acquired the ability to invade surrounding

tissues

Metastasis- secondary tumor away from the site of the “primary” tumor

circulating tumor cells (CTCs)- cell that’s travel through an individual

clonality-

chromosomal translocation

Philadelphia chromosome

somatic mutations- because they are mutations in somatic cells

epigenetic changes- persistent changes in gene expression caused by modifications to chromatin

structure without altering the chromosomes sequence

dominant clones- offspring of the best adapted cells will produce those

genetic instability

contact inhibited- i.e., cell growth tends to be inhibited by extensive contact with other cells

replicative senescence-

telomerase

driver mutation causative changes/mutations that drive cancer progression