Enzymes, coactivators/repressors, pathways and locations

eIF2

GTP bound GTPase that initiates translation by moving ribosome until it finds the AUG codon. Its activity is regulated by eIF2B and GTP—when it gets phosphorylated, eIF2B cannot GEF it

CAP

Catabolite Activator Protein, present in prokaryotic lac operon transcription. Serves to increase DNA binding site affinity with RNAP, has a helix-helix turn to bind with site promoter (not cis element). cAMP is its coactivator

NtrC

A prokaryotic transcription regulator bound to a distant cis element (several hundred away). Once RNAP is at the promoter site, NtrC “kisses” the promoter to set transcription off. The DNA acts as a tether, making “falling” onto the promoter less random

Guanine (attenuation)

“transcription regulator”. Mid-transcription, the mRNA coding for guanine production forms a riboswitch. When guanine levels are high and guanine binds the riboswitch, it renders the RNAP unable to continue, causing premature termination

cI

Lambda repressor protein. It blocks the Cro operator but has a dual function as its own activator–its binding directs RNAP to transcribe more of itself, keeping the virus in prophage. Most of the bacteriophage DNA is left UNTRANSCRIBED.

Cro

Protein in Lambda Virus, initiates lytic phase. When the Induction Event occurs (stopping Lambda synthesis) Cro will bind to the shared operator, blocking cI transccription and induces a positive feedback loop of its own transcription. Most Viral dna is extensively transcribed now

RNAP1

Eukaryotic RNAP, transcribes rRNA

RNAP2

Eukaryotic RNAP, transcribes mRNA

RNAP3

Eukaryotic RNA, transcribes tRNA

TFIID

General transcription factor for mRNA, TATA box recognizer in eukes. First transcription factor to bind to DNA. Works with TFIIB, TFIIA, and later TFIIE and TFIIH. It stays in place as the RNAP2 zooms. Reviews code after histone loosening

TBP

TATA binding protein, subunit of TFIID. Finds the TATA box that is upstream of the start site

TFIIB and TFIIA

Gen transcription factors for mRNA. Joins D, A, and B to attract RNAP2. Leave with TFIIH and TFIIE as elongation begins

TFIIE and TFIIH

Gen transcription factors for mRNA. With TFIID, introduce kink in DNA. Leave with TFIIH and TFIIE as elongation begins

CRC (Chromatin Remodling Complex)

Protein complex that winds and unwinds the DNA around histone cores. ATP dependent, used in nucleosome sliding (to make DNA accessible) and after Histone Modifying Enzymes

CTD

C terminal domain of RNAP2. Repetitive repeats, calls CPSF and CstF to AAAA the mRNA tail

CPSF

Cleavage Polyadenylation Specificity Factor. Attached to the AAUAAA at the 3’ end of the mRNA (with CstF) to call PAP.

CstF

Cleavage Stimulation factor. Attached to the AAUAAA at the 3’ end of the mRNA (with CPSF) to call PAP. Helps cut coded end off as PAP produces A tail

Holoenzyme (prokaryote)

Made up of core protein and sigma factor. Work together in the abortive phase

Mediator

Protein on top of the RNAP complex in euaryotes, mediate the strength of responses to activators or repressors based on number and etc.

HAT

Histone Acetyltransferase. Transfers acetyls onto K9 and K8 of H3 and H4 respectively, then after HK phosphorylates Ser10, it acetyls K14 of H3 to finish unbinding

HK

Histone Kinase. After first acetyls are transferred, it phosphorylates Ser10 of H3 during indirect gene activation

Histone Methyltransferase

Called by repressive reader of histones. Methylates cystines on nearby DNA, making all tight

Deacetylase

Deacetylases Ks on histone subunits 3 and 4, retightening them

Special: IC50

[ ] of compound needed to reduce expression of a trait by 50%

CBC

Cap binding complex. Adds G-cap to 5’ mRNA

EJC

Exon Junction Complex. Marks locations of splicing occurence, “bulldozed” off by RNAP2. If any are left, it calls for RNA degradation because that means an intron and a nonsense code was left in

Spliceosome

Complex of RNA and proteins responsible for splicing mRNA

Sxl

Sex lethal protein. Only functional when Sxl mRNA splicing is positively (ish) controlled–blocks Tra splicing in turn.

Tra protein

Transformer in Drosphilia. Only produced by positive splicing control, the protein blocks Dsx (double sex) splicing.

Dsx

Protein produced by double sex. Under default, is a female suppressant. After positive splicing control from Tra (removing one of the splicing regions but not both) it becomes a male suppressant

PAP

Poly adenylation protein. Is called by CstF and CPSF, then coats the tail it creates

“Cropping” protein

Cuts the Gcap and Atail off a microRNA (as shown in image). Afterwards, it is further cut by a “Dicer”

“Dicer” protein

Cuts the internal loop off of miRNA after the “Cropper” does its work. Afterwards, miRNA binds with Argonaut and other proteins

Also cuts double-stranded viral RNA to produce siRNA, (basically at the same phase as miRNA post cropping and dicing)

Argonaut

Binds with miRNA (after Cropping and Dicing) AND siRNA to create RISC

RISC (miRNA and siRNA)

RNA induced silencing complex. IN eukaryotes, matches to other RNAs and degrades them. If close match, full degradation. It partial, repression, trans suppression, EVENTUAL degradation

RITS

Binds with siRNA, looks for viral mRNAs while being made–thus, targets viral DNA. It silences them through chromatin modifying enzymes that methylate them

Chromatin Modifying Enzymes (RITS)

Called for by RITS to methylate viral chromatin, rendering it silent

Translational repressor protein (SD)

Binds to a hairpin on the RNA sequence in a way that blocks the SD sequence. Differes from temp switch, riboswitch, and antisense rna reglatory mechanisms of translation

Chaperonin

HSP60

HSP60

Second line of folding defense. Double barrel that holds a misfolded protein until it finally folds and gets better. ATP dependent to close the Gro5S cap

HSP70

Binds to hydrophobic regions of proteins (formed in cytosol) to shield them. They also use ATP hydrolysis to generate energy to help with folding .

Also–transports mitochondrial and chloroplast proteins to TOM/TOC

Proteasome

Abundant complex that degrades polyubiqiutin-marked proteins. It is a hollow cylinder with unfoldase caps on both ends and an active site at its center. The unfoldase rings associate with the ubiquitin

Gro5S

Cap for Hsp60

E1

U-activating enzyme. Is ATP dependent when binding with Ubiquitin, turns a thiol into S-C=O when binding to the C-terminus of Ubiquitin. Afterwards, binds with E2, and trades functional groups

E2

U-conjugating enzyme. After associating with E1 and trading its thiol for S-C=O (the ubiquitin attached on the O)

E3

U-Ligase. Binds to degradation sequences (exposed hphobic sequences) and forms a complex with E2. Then helps to transfer Ubi onto the protein of interest.

PKA

Protein Kinase A. Has four subunits, two inactive–when cAMP binds to the two inactive units the two active subunits dissaciate and become reactive. They enter the nucleus to activate CRE elements, blocking glycogen synthase and promoting glycogen phosphorylation kinase.

CRE elements

“cAMP responsive elements” – occur when adrenaline happens. Include CREB and CBP

CREB

Cre Binding Protein. Activates the cAMP response elements, and is coactivated by CBP

CBP

Creb-Binding Protein. Coactivates CREB, does NOT touch the DNA

Special: Monoubiquitination

Marked for Histone Regulation

Special: Multi Ubiquitination

Marked for Endocytosis

Special: Polyubiqituination on Lys48

Proteasomal degradation

Special: Polyubiqituination on Lys63

DNA Repair

GPCR

Membrane protein and receptor for adrenaline. Activates G protein, which activates adenyl cyclase, which makes ATP

Ran GTPase

Binds to importer/exporter for proteins entering/leaving the nucleus. They are activated (GTP) entering the nucleus but deactivated (GDP) when leaving. Uses NTF2 to translocate into nucleus

RanGef

Bound to chromatin, exchanges GDP for GTP as the Ran-GTPase enters the nucleoporin.

Ran-GAP

GTP-ase Activating Protein, works with Ran Binding Protein to promote release of cargo/receptor in the cytosol

NLS

Nuclear Locator Signal. Rich in Lysine and Arginine, binds to Nuclear Importer proteins

NES

Nuclear exporter signal. Rich in Leucine, binds to Nuclear exporters

Ran Binding Protein

Works with Ran GAP to promote hydrolysis in RanGTPase and make it release cargo/its receptor

Calcenurin

A protein phosphatase. Induces a conformational change in T-cells when [Ca2+] is high, as it binds to NF-AT, dephosphorylates it, and exposes its NLS region previously hidden by phosphorylation, allowing it to travel to the nucleus in times of attack

NF-AT

Nuclear Factor of Activated T Cells. Has both NES and NLS–in low calcium, it exists in cytosol and phosphorylated. In high calcium, calcenurin dephoses it, binds to it, exposes its NLS, making a nuclear importer and NTF2 take it in. When calcium decreases, calcenurin dissassociates and it reveals an NES, so it is taken back out

TIM23

Internal Mitochondrial Translocon. Has a signal peptidase to cut off the N-terminal amphipathic alpha helix in the transported protein

Oligosacchryl transferase

Transmembrane protein next to the ER Translocon that transfers oligosacharrides to Asn (N) in lumen during translation. Looks for Asn-X-Serine or Asn-X-Thr

ER Mannosidase

Removes one mannose from oligosaccharide after the removal of three glucoses, IN THE LUMEN. It is then transferred to the Golgi

Calnexin

Transmembrane protein in the ER membrane, binds to the last glucose on an oligosaccharide and helps with folding

Glucosyl transferase

Checks that completed oligosacharride attached proteins are completely folded. If not, they attach a new glucose from UDP glucose and makes it go to Calnexin again

y-COP

Inner subunit in COP1. It binds to Arf GAP, enabling GTP hydrolysis in ArfGTP to release the vesicle from the ER

Arf GTP

GTPase that signals for COP1 coat assembly. It is activated by Arf GEF receptors in the membrane

Sar1 GTP

GTPase that signals for COP2 and Clathrin coat assembly. It is activated by Sar1 GEF receptors in the membrane

Sec23

Inner subunit in COP2, and stimulated by outer two subunits 13/31. Has GTPase activity and cleaves Sar1GTP to initiate release

Dynamin

Used for clathrin coat release (from trans golgi N). Specifically for pinching off

Auxillin and HSP70

Used to uncoat clathrin coats

Rap GTP

Protein on Vesicle membrane. Binds to Rab effector to dock/snare vesicles

NSF

Unravels v-t-snare complex once it has finished work (with adapters). V snare can be destroyed or reused. IS ATP DEPENDENT

Soluble ER protein signal

KDEL

KDEL receptor

Binds to KDEL of soluble ER proteins in LOW pH. Binds to Cop1 inner memb proteins

Er Memb Protein Retrieval Signal

KKXX at C terminus, binds directly to COP1 inner subunits

Tethering proteins

Hold transport vesicles to golgi cisternae with tethering proteins

Lysosomal Hlase Precursor (before golgi)

Nterminal NLinked oligosaccaride protein.

Phoso-N-acetyl glucosamine

Added to lysosomal hydrolase precursor in early golgi. N-acetyl glucosamine is removed later in cis golgi

M6P

Protein additional group delivered to hydrolase, made from the Phoso-N-acetyl glucosamine. Taken up (with their proteins) in TGN by M6P receptors, which dissociate at high pH in the endosomes.

eIF4G

Binds to poly A tail to start tranbslation