BMB424-EX2 Flashcards

Uses Cdt1 (G1 phase = red) and Geminin → (S/G2/M phases = green)

yellow = transition

Uses synthetic nucleoside analog of thymidine, then use antibodies against BrdU

sees where replicating DNA is

flourencent

recognize polyubiquitin

recycle ubiquitin

unfolding

chymotrypsin --> cut after hydrophobic

Trypsin --> cut after basic

Caspase --> cutes after acidic

Mono - attach 1 ub (trafficking)

Multi - multiple sites (endocytosis)

Poly - long chain of ub (degradation)

The longer a protein can be associated with the regulatory subunit of the
proteosome, the more likely the protein is going to be degraded

rRNA is most of the ribosome

catalyzes bind formation for speedy translation

anticodon bonds to only specific mRNA+tRNA

signal

sends info from one cell to another

protein on target cell to receive signal

Relayer

Chain reaction to pass message along

cell changing

switching between on + off

GTP binding (bound to GTP = ON)

receptors unique to certain signals

different downstream proteins

26S Proteasome --> degradation of proteins

ubiquitination doesn't equal immediate degradation (dwell time)

More reads/higher density = more ribosome

clustered in codon reading = active translation

peaks at start codon = initiation

ribosome slowing or stalling to read

High mRNA + low ribosome = inefficient

outputs make the process faster

cell division

On diagram: loops, plus signs, promoting production

outputs shut down process

inhibition

blunt ends, minus signs, product shuts down production

creates distinct regions in chromatin regulation

keeps charge

changes protein - protein interactions

neutralizes charge (+ histones hugging - DNA)

opens chromatin to activate genes

adding sugars for folding, stability, and recognition

ID in ER

adds large - charged group

on/off switch

assembles large proteins into complexes

G1/s - transition/start (size? environment? density? attachment?)

G2/M - mitosis (replicated? environment?)

Meta to Ana - cytokinesis (chromosomes attached? ready to split?)

G1 - high levels = expression of G1/S cyclins

G1/S - activate cdk to push cell into S phase for cell cycle entry

S - stimulate chromosome duplication

M - enter mitosis at G2/M and degrade at meta to ana

EF1

escorts tRNA to A site

EF2

uses GTP hydrolysis to provide mechanical push of ribosome forward

Stop codons

entry for secretory pathway

use vesicles to go to golgi apparatus

sends to final destination

Manufacture - lipids + export proteins

Quality control - check proteins before fold

Storage - store Ca²⁺ for signal

BiP - helpers - grab floppy proteins and folds correctly

Disulfide bonds - staples - keep together

water freezing aa comes out > SRP grabs ribosomes to stop > SRP receptot docks ribosome > translocator in membrane for protein

Start transfer - opens door for threading

Stop transfer - closes door for threading

Standard signal usually cut off

N term in ER with C term in cytosol (BC C is +)

Ion channels

g protein using (GPCR)

enzyme coupled

molecules that spread signals deep into a cell after receptor activation

cAMP

Fast - exocytosis

Slow - cell cycle entry

Gs - activates adenylyl cyclase

Gi - inhibits adenylyl cyclase

ligand binds to GCPR > GDP kicked out > GTP let in > split into a and B > signal stops once a subunit times out > GTP turned back to GDP

26S proteasome is processive because it binds, unfolds, translocates, and fully degrades proteins in one continuous operation without releasing them halfway

E1 picks up + activates Ub with ATP > E2 carries live Ub from E1 to E3 > E3 acts as a matchmaker for Ub and specific target protein

UBE20 binds best with Ub and NAP1L1

NF-kB family of transcription factors

noncanonical path implicated in regulating cell signaling

high density = stop cell division

Measure translation genome wide at single codon resolution

Small N term, large C term, active site in middle

T loop regulation (phosphorylated = moving loop and active site to be available)

changing location/activity

bridge between mRNA codon + aa

anticodon binds w tRNA

initial Ub binding

ub removal + 19S activation

removing final Ub

substrate binding + unfolding

20s gate open

A - aminoacyl - charged tRNA entry

P - peptidyl - holding tRNA attached to growing polypeptide

E - exit - uncharged DNA

anchors protein to cell membrane since fats like to be near each other

assembles miotic spindles

ensure sister chromatids apart

chromosome condensation

break down of nuclear envelope

freeze ribosome > lyse cells > digest unprotected RNA > isolate ribosome > convert to cRNA > sequence > align

cell division regulating proteins

activated when needed

phosphorylates T loop

wee1 adds P but not active til cell is ready

cdc25 removes inhibiting P --> burst of energy

DUBs > removing Ub to recycle

Narrow 20S gate

Interphase (G1, S, G2) - growing, synthesizing, growing

M phase - mitosis

Cytokinesis - splitting

Chromosome condense

nuclear envelope breaks

chromosomes line up in middle

sister chromatins pulled apart

2 nucli formed

phosphorylates target

T loop can expose active site

catalyzes ub in exit of mitosis

cleans up

ends cell division and destroys proteins w cyclins

P21 - safety brake - stops if DNA damaged

P27 - stop and stay - signal to stop growth in G1

cdc20 - triggers ACP/C activity

cdh1 - maintains ACP/C activity after anaphase

clean up

destroys P27 so cell can move from G1 to S

target must be phosphorylated

cdk1 + M cyclin = inactive M cdk

CAK + wee1 + inactive M cdk = inactive M cdk with active P and inhibiting P

cdc25 takes inhibiting P and creates active M cdk

cdh1 - keeps cyclin levels low so cell can grow and not reenter S phase

cdh20 - destroys securin + M cyclins

G1 - cdk4/6 - cyclin D - kicks off mitosis

G1/S - cdk2 - cyclin E - push cell past start

S - cdk2 - cyclin A - triggers DNA replication

M - cdk1 - cyclin B - cell division

K11 -marks cyclins for rapid degradation in mitosis

K63 - DNA repair

K48 - degrade proteasome, unfolds so protein can be shredded

K29/33 - protein trafficking