Midterm 1 revision Flashcards
Where’s TATA box found?
In the promoter region
Where do coactivator complexes function at?
Coactivator complexes function at or near the promoter’s TATA box.
Signal is __ interaction between ligand and receptor
Signal is non-covalent interaction between ligand and receptor
How can PKA be deactivated?
Option 1: cAMP is converted to AMP by cyclic nucleotide phosphodiesterase
Option 2: GAPs (GTPase activator proteins) and RGS (Regulators of GTP signaling) determine how long the switch remains on
Describe desentization
Ga leaves, leaving G-beta and G-gamma behind
Bark can phosphorylate Ser on cytoplasmic carboxylic end
Phosphorylated end interacts with Barr (B-arrestin) protein which results in endocytosis of the receptor making it unavailable
Describe integration
Gi inhibits adenylyl cyclase
Thus depending on concentrations of Gs and Gi adenylyl cyclase will either be activated or inhibited
Gq stimulates the action of ___
Gq stimulates the action of protein lipase C
Neurotransmitter usually act through ___ pathway
Neurotransmitter usually act through IP3 and Ca2+ pathway
Describe MAPK pathway
- Insulin binds to RTK. Results in phosphorylation of cytoplasmic domain of the receptor on its carboxyl-terminal Tyr residues
- This phosphorylation results in another phosphorylation of IRS-1 protein on its Tyr residues, activating it
- IRS-1 now acts as a docking protein. Adaptor protein allows other adaptor protein to bind. Allows another adaptor protein Grb2 to bind to Tyr of IRS-1
- Irs-1> Gb2->Sos-> Ras-> Raf-1
- Raf-1 phosphorylates MEK on two Ser residues, activating it. MEK phosphorylates ERK on a Thr and a Tyr residue, activating it.
Activated ERK can act as kinase - ERK moves into the nucleus and phosphorylates nuclear transcription factors such as Elk1, activating them
- Elk1 joins SRF to stimulate the transcription and translation of a set of genes
Describe PIP3 pathway
- Ligand binds to a receptor, IRS1 is phosphorylated and acts as a docking protein
- IRS1 allows for PI3K (PI3 kinase) to bind
- PI3K converts PIP2 to PIP3 by adding a phosphate group- phosphorylation of 3rd carbon (see next slide)
- PIP3 allows for docking of PKB (protein kinase B)
- PKB is activated by phosphorylation
- On target of PKB is GSK3. Phosphate group is added to GSK3 INACTIVATING it. Phosphorylation is a modulation step - can both activate & inactivate
- GSK3 is a GS (glycogen synthase) kinase. It is active only when it is not phosphorylated. In its active state can add phosphate to glycogen synthase. GS converts glucose to glycogen. GS is active when it is NOT phosphorylated. The moment it is phosphorylated, it becomes inactive. - remover of an activator step
Insulin thus promotes glycogen synthesis
PKB stimulates ___
PKB stimulates the movement of GLUT4- glucose transporter- into the plasma membrane
Cross talk- explain
Option 1: RTK phosphorylates 2 Tyr residues on b-androgenic receptor and through PKB causes phosphorylation of 2 Syr residues. This results in internalization of the androgenic receptor
Option 2: RTK phosphorylates GPCR on Tyr creating a point of nucleation for activation of MAPK cascade-> enhancement of a signal
Hormones that trigger RTK are usually ___
Hormones that trigger RTK are usually cytokines
What do cytokines do?
Inhibit other ligan function
What are the 3 common AA phosphorylated by kinases?
Tyrosine
Serine
Threonine
What 2 elements do kinases have?
ATP binding site
Catalytic cleft
What is the direction of ion movement through the ion channels and the reason for their movement?
Na+ and Ca2+ move into the cell; K+ moves outside the cell - in the direction of the chemical gradient
Cl- moves out of the cell against the chemical gradient, but down the electrical gradient
Where is action potential can be found?
Across synapse and within the axon
How does the termination of nerve impulse occur?
- Achieved by the voltage-gated calcium channels that are gated by changes in membrane potential
- Calcium enters the cell-> causes depolarization+ acts as a second messenger
- Causes secretory vesicles with neurotransmitters to be exocytosed into the cytoplasmic cleft
- Neurotransmitters allow cations to go from outside to inside-> cause depolarization
Which neurotransmitters allow the influx of cations? Anions?
Anions- glycine
Cations- acetylcholine, serotonin, glutamate
What are the ligands of nuclear receptors?
Steroids, Thyroid hormones, Vitamin D, retinoic acid
Autocrine-definition
Chemicals produced by a cell that acton the same cells
Paracrine- definition
Chemical that act on the cells that are nearby
Name bioactive lipids
Sterols
Prenols
Sphingolipids
Glycerophospholipids
What are glycerophosphates precursors of?
Inositol phosphates
Pip2-> IP3 + DAG (phospholipase C)
PIPI2-> PIP3 (PI3K)
How does IP3 stimulate glycogen breakdown?
- GPCR interacts with a ligand-> goes to activate its target
- Its target is PLC which cleaves PIP2 into IP3 and DAG
- IP3 causes a release of Ca2+. Ca2+ activates calmodulin
- Calmodulin is an effector
which leads to a signalling cascade that activates an enzyme phosphorylase kinase - Phosphorylase kinase activates glycogen phosphorylase
- Glycogen phosphorylase cleaves off glucose molecules from glycogen polymers.
Which enzymes determine the blood group?
Glycosyltransferases
Eicosanoids are ___ factors
Eicosanoids are paracrine factors
How do NSAIDs function?
Inhibit cyclooxygenases (COX 1 and 2) thus inhibitign the production of prostoglandins and thromboxanes
Arachidonic acid is released from ___ with the use of –
Arachidonic acid is released from glycerophospholipids with the use of phospholipase A2
How do we sense ight?
all-trans-retinol-> rhodopsin-> all-trans-retinal
Which forms of vit a are interconvertible?
retinal and retinol
Which nuclear receptors are involved in vit a?
Retinoic acid receptor (RAR)
Retinoid X receptor (RXR)
RNA pol binds at ___
Rna pol binds at promoter
What is the bondign between DNA and regulatory proteins?
Hydrogen bonding
What are the AA most commonly involved in hydrogen bonign between proteisn and DNA?
Asn Gln Glu Lys Arg
Describe leusine zipper
Partially interacts with DNA via Lys/Arg residued based on negatively charged phosphates
Which 2 domains do regulatory proteins have?
DNA binding and protein-interaction
What is chromatin?
DNA + Histone (H1, H2, H2B, H3, H4)
What is the function of SW1 and SNF enzymes?
Delete H1 and add histone variants such as H3.3 and H2AZ
Name histone modification and their locations
Methylation (lys and arg)
Acetylation (lys)
Phosphorylation (thr and serine)
Ubiquination and sumoylation (lys)
What is acetylation of histones regulated by?
HAT and HDAC
HAT makes DNA more accesible
May also prevent or promote interaction with other proteisn involved in transcription or its regulation
Modifications can occur only when chromatin is __
Modifications can occur only when chromatin is open
Describe single DNA modifcation
Methylation at CpG sequnce
Inhibits access to promoter region
TFIIB is a ___
TFIIB is a coactivator
What’s the role of activators?
- Decide which genes are going to be activated
- Are able to initiate histone nucleosome modifications
Mediators bind to ___
Mediators bind to CTD
What is the role of TFIIH?
Phosphorylates CTD and helps pol ii to move forward
UAS are the same as __ in yeast
UAS are the same as enhancers in yeast
Nuclear receptors can be further regulated by ___ and __
Nuclear receptors can be further regulated by phosphorylation and methylation
Nuclear receptors have __ domain
Nuclear receptors have zinc-finger domain
How and where are type I nuclear receptors found
Found in the cytoplasm inactivated due to bound Hsp-70s
What are the translation repressors?
RNA-binding proteins that bind to specific sites in the 3’ untranslated region of mRNA- prevent or slow down translation
Which metal is a cofactor for RNA synthesis?
Mg2+
Describe sigma cycle
- Initial TF - sigma factor- binds to promoter region which helps to bring in pol II- initiation
- Promoter leaves, sigma leaves
- NusA comes in to help pol II to move forward- elongation
- Termination - NusA and pol ii leave
What are the 2 types of RNA pol?
pol I: synthesis of rRNA
pol II: synthesis of mRNA, specialized RNA e.g. microRNA
pol III: synthesis of tRNAs, 5s rRNA and specialized RNA
Assebmly stage in transcription
- TBP and TFIIB bind to promoter region
- preinitiaotin complex if fomed wiht 12 other basal TF
- Helicase activity forms transciption bubble
Initiation stage in transcription
CTD is phosphorylated by TFIIH allowign pol II to initiate transcritption
Elongation stage in transcription
TFIIH and TF leave
Elongation factors are required for pol II to move forward
Termination stage in transcription
Elongation factors leave
Termination factors facilitate the process
5’ cap process
- Phosphohydrolase removes 1 phosphate group from mRNA 5’ end making it diphosphate
- Guanylyl tranasferase brings in GTP, removes 2 phosphates and adds the rest to 5’ end of mRNA through unusual 5,5-triphosphate linkage
- Methyl group is added by guanine-7-methyltransferase
- 3 capping enzymes are associated with CTD of pol II until the cap is synthesized. The capped 5’ is released from capping enzymes and is boudn to cap binding complex- keeps cap bound to CTD until the end of transcription
Histones don’t have __
Histones don’t have introns
Describe self-splicign
Doesn’t require energy
Requires guanosine co-factor; UA 5’ sequnce and GU 3’ sequnce
1. The 3’ OH of guanosine (GTP) acts as a nucleophile, attacking the phosphate at the 5’ splice site breaking phosphodiester bond between UA
The guanosine 3-hydroxyl group forms a normal 3,5-phosphodiester bond with the 5’ end of the intron
The 3’ OH of the 5’ exon becomes the nucleophile, completing the reaction.
UU bond
Descibe splicing by spliceosome
Occurs in most mRNA (3 groups of introns)
U1 binds to GU (donor site) and U2 binds to A at branching site- requires energy
U4 and U6 bind with help of ATP
U5 binds to AG (acceptor site) completing the spliceosome
GU and A are brought together to bond and form a lariat
This frees up 3’ OH of exon which can attack 3’ end of intron
What makes up a spliceosome?
Spliceosome is made of snRNP’s: U1, U2, U4, U5 and U6
What are the 3 structures of Nucleotides sequences in introns that are spliced by Spliceosome
- Donor site: 5’ end of intron has dinucleotide G-U
- Acceptor site: 3’ end has A-G dinucleotide (2 nucleotides)
- Branching site: Upstream of 5’ end there is sequence that is identified by A
Describe makign of ploy(A)tail
Adaptor proteisn and enzymes come together at cleave sequence were polyadenylyl polyemerase and endonuclease form a comples -> cleavage
Followed by synthesis of Poly(A)tail
What does adaptor do?
Reads a triplet and is complimentary to it 1
What are the termination codons?
UAG, UGA and UAA- nonsense codons
What is the initiaiton codon
AUG
what are the 2 AA that only have 1 codon
Met and Trp
How does genetic code differs in mitochondria?
UGA encodes for Trp instead of stop
AAG and AGA encodes for stop instead of arginine
tRNa have __ on 3’ end- expand on this
tRNa have CCA on 3’ end
Added at post-translation modification
Attachment point for AA
Descrieb aminoacetylation of tRNA
Carboxyl end of amino acid attack an alpha phosphate of ATP- removes 2 phosphate group, attaches to the rest and becomes activated -> 5’ Aminoacyl adenylate
5’ Aminoacyl adenylate is ready for attachment to tRNA which is done by 2 classes of aminoacyl-tRNA synthetases
Class 1: aminoacyl group is initially transferred to 2’- hydroxyl group of 3’ terminal residue then to 3’ hydroxyl group by transesterification
Class 2: aminoacyl group is transferred directly to the 3’ hydroxyl group of the terminal adenylate
Initiation of translation in eukaryotes
- elF1A (A site) and elF3 bind to 40s subunit
elF1 binds to E site
tRNA with met is boudn to elF2 + GTP
elf5B-GTP binds completing preinitiaiton complex - mRNA is brought in by elF4F. mRNA attachement to preinitiaiton complex requires energy
- mRNA is scanned until AUG codon is reached, startign from 5’ cap
- Large 60s subunit comes in
Describe peptide bond formation
- Initiation Met is transferred from its tRNA to the amino group of the second AA in the A site
- Now there’s a dipeptidyl tRNA in the A site and unchraged tRNA in the P site
- Peptidyl transferase catalyses peptide bond formation
tRNA at A site is pushed to P site
Which factor helps in peptide bond formation?
Elongation factor P (EF-P)
Factor participating in translocation
EF-G-GTP pushes dipeptidyl-tRNA to P site. A site becomes available
Describe termination in translation
Occurs when nonsence codon arrives at A site
Release factors bind to A site releasing newly made peptide from P site
Name release factors
RF1, RF2 and RF3
What is RRF?
Ribosomal recycle factor- uses elongation factors and energy to dissaccosiate transaltional machinery
Role of IF3
Remains attached to small subunit
Helps to reuse translational machinery
Protein degradation
Attachement of Ubiquitin to lysine
E1-> E2->E3-> lysine
