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BC 2- > Midterm 1 revision > Flashcards

Midterm 1 revision Flashcards

1
Q

Where’s TATA box found?

A

In the promoter region

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2
Q

Where do coactivator complexes function at?

A

Coactivator complexes function at or near the promoter’s TATA box.

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3
Q

Signal is __ interaction between ligand and receptor

A

Signal is non-covalent interaction between ligand and receptor

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4
Q

How can PKA be deactivated?

A

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

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5
Q

Describe desentization

A

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

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6
Q

Describe integration

A

Gi inhibits adenylyl cyclase

Thus depending on concentrations of Gs and Gi adenylyl cyclase will either be activated or inhibited

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7
Q

Gq stimulates the action of ___

A

Gq stimulates the action of protein lipase C

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8
Q

Neurotransmitter usually act through ___ pathway

A

Neurotransmitter usually act through IP3 and Ca2+ pathway

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9
Q

Describe MAPK pathway

A
  1. Insulin binds to RTK. Results in phosphorylation of cytoplasmic domain of the receptor on its carboxyl-terminal Tyr residues
  2. This phosphorylation results in another phosphorylation of IRS-1 protein on its Tyr residues, activating it
  3. 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
  4. Irs-1> Gb2->Sos-> Ras-> Raf-1
  5. 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
  6. ERK moves into the nucleus and phosphorylates nuclear transcription factors such as Elk1, activating them
  7. Elk1 joins SRF to stimulate the transcription and translation of a set of genes
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10
Q

Describe PIP3 pathway

A
  1. Ligand binds to a receptor, IRS1 is phosphorylated and acts as a docking protein
  2. IRS1 allows for PI3K (PI3 kinase) to bind
  3. PI3K converts PIP2 to PIP3 by adding a phosphate group- phosphorylation of 3rd carbon (see next slide)
  4. PIP3 allows for docking of PKB (protein kinase B)
  5. PKB is activated by phosphorylation
  6. On target of PKB is GSK3. Phosphate group is added to GSK3 INACTIVATING it. Phosphorylation is a modulation step - can both activate & inactivate
  7. 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
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11
Q

PKB stimulates ___

A

PKB stimulates the movement of GLUT4- glucose transporter- into the plasma membrane

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12
Q

Cross talk- explain

A

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

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13
Q

Hormones that trigger RTK are usually ___

A

Hormones that trigger RTK are usually cytokines

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14
Q

What do cytokines do?

A

Inhibit other ligan function

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15
Q

What are the 3 common AA phosphorylated by kinases?

A

Tyrosine
Serine
Threonine

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16
Q

What 2 elements do kinases have?

A

ATP binding site

Catalytic cleft

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17
Q

What is the direction of ion movement through the ion channels and the reason for their movement?

A

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

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18
Q

Where is action potential can be found?

A

Across synapse and within the axon

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19
Q

How does the termination of nerve impulse occur?

A
  • 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
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20
Q

Which neurotransmitters allow the influx of cations? Anions?

A

Anions- glycine

Cations- acetylcholine, serotonin, glutamate

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21
Q

What are the ligands of nuclear receptors?

A

Steroids, Thyroid hormones, Vitamin D, retinoic acid

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22
Q

Autocrine-definition

A

Chemicals produced by a cell that acton the same cells

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23
Q

Paracrine- definition

A

Chemical that act on the cells that are nearby

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24
Q

Name bioactive lipids

A

Sterols
Prenols
Sphingolipids
Glycerophospholipids

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25
Q

What are glycerophosphates precursors of?

A

Inositol phosphates
Pip2-> IP3 + DAG (phospholipase C)
PIPI2-> PIP3 (PI3K)

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26
Q

How does IP3 stimulate glycogen breakdown?

A
  1. GPCR interacts with a ligand-> goes to activate its target
  2. Its target is PLC which cleaves PIP2 into IP3 and DAG
  3. IP3 causes a release of Ca2+. Ca2+ activates calmodulin
  4. Calmodulin is an effector
    which leads to a signalling cascade that activates an enzyme phosphorylase kinase
  5. Phosphorylase kinase activates glycogen phosphorylase
  6. Glycogen phosphorylase cleaves off glucose molecules from glycogen polymers.
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27
Q

Which enzymes determine the blood group?

A

Glycosyltransferases

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28
Q

Eicosanoids are ___ factors

A

Eicosanoids are paracrine factors

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29
Q

How do NSAIDs function?

A

Inhibit cyclooxygenases (COX 1 and 2) thus inhibitign the production of prostoglandins and thromboxanes

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30
Q

Arachidonic acid is released from ___ with the use of –

A

Arachidonic acid is released from glycerophospholipids with the use of phospholipase A2

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31
Q

How do we sense ight?

A

all-trans-retinol-> rhodopsin-> all-trans-retinal

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32
Q

Which forms of vit a are interconvertible?

A

retinal and retinol

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33
Q

Which nuclear receptors are involved in vit a?

A

Retinoic acid receptor (RAR)

Retinoid X receptor (RXR)

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34
Q

RNA pol binds at ___

A

Rna pol binds at promoter

35
Q

What is the bondign between DNA and regulatory proteins?

A

Hydrogen bonding

36
Q

What are the AA most commonly involved in hydrogen bonign between proteisn and DNA?

A 
Asn
Gln
Glu
Lys
Arg
37
Q

Describe leusine zipper

A

Partially interacts with DNA via Lys/Arg residued based on negatively charged phosphates

38
Q

Which 2 domains do regulatory proteins have?

A

DNA binding and protein-interaction

39
Q

What is chromatin?

A

DNA + Histone (H1, H2, H2B, H3, H4)

40
Q

What is the function of SW1 and SNF enzymes?

A

Delete H1 and add histone variants such as H3.3 and H2AZ

41
Q

Name histone modification and their locations

A

Methylation (lys and arg)
Acetylation (lys)
Phosphorylation (thr and serine)
Ubiquination and sumoylation (lys)

42
Q

What is acetylation of histones regulated by?

A

HAT and HDAC
HAT makes DNA more accesible
May also prevent or promote interaction with other proteisn involved in transcription or its regulation

43
Q

Modifications can occur only when chromatin is __

A

Modifications can occur only when chromatin is open

44
Q

Describe single DNA modifcation

A

Methylation at CpG sequnce

Inhibits access to promoter region

45
Q

TFIIB is a ___

A

TFIIB is a coactivator

46
Q

What’s the role of activators?

A
  • Decide which genes are going to be activated

- Are able to initiate histone nucleosome modifications

47
Q

Mediators bind to ___

A

Mediators bind to CTD

48
Q

What is the role of TFIIH?

A

Phosphorylates CTD and helps pol ii to move forward

49
Q

UAS are the same as __ in yeast

A

UAS are the same as enhancers in yeast

50
Q

Nuclear receptors can be further regulated by ___ and __

A

Nuclear receptors can be further regulated by phosphorylation and methylation

51
Q

Nuclear receptors have __ domain

A

Nuclear receptors have zinc-finger domain

52
Q

How and where are type I nuclear receptors found

A

Found in the cytoplasm inactivated due to bound Hsp-70s

53
Q

What are the translation repressors?

A

RNA-binding proteins that bind to specific sites in the 3’ untranslated region of mRNA- prevent or slow down translation

54
Q

Which metal is a cofactor for RNA synthesis?

A

Mg2+

55
Q

Describe sigma cycle

A
  1. Initial TF - sigma factor- binds to promoter region which helps to bring in pol II- initiation
  2. Promoter leaves, sigma leaves
  3. NusA comes in to help pol II to move forward- elongation
  4. Termination - NusA and pol ii leave
56
Q

What are the 2 types of RNA pol?

A

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

57
Q

Assebmly stage in transcription

A
  1. TBP and TFIIB bind to promoter region
  2. preinitiaotin complex if fomed wiht 12 other basal TF
  3. Helicase activity forms transciption bubble
58
Q

Initiation stage in transcription

A

CTD is phosphorylated by TFIIH allowign pol II to initiate transcritption

59
Q

Elongation stage in transcription

A

TFIIH and TF leave

Elongation factors are required for pol II to move forward

60
Q

Termination stage in transcription

A

Elongation factors leave

Termination factors facilitate the process

61
Q

5’ cap process

A
  1. Phosphohydrolase removes 1 phosphate group from mRNA 5’ end making it diphosphate
  2. Guanylyl tranasferase brings in GTP, removes 2 phosphates and adds the rest to 5’ end of mRNA through unusual 5,5-triphosphate linkage
  3. Methyl group is added by guanine-7-methyltransferase
  4. 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
62
Q

Histones don’t have __

A

Histones don’t have introns

63
Q

Describe self-splicign

A

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

64
Q

Descibe splicing by spliceosome

A

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

65
Q

What makes up a spliceosome?

A

Spliceosome is made of snRNP’s: U1, U2, U4, U5 and U6

66
Q

What are the 3 structures of Nucleotides sequences in introns that are spliced by Spliceosome

A
  1. Donor site: 5’ end of intron has dinucleotide G-U
    1. Acceptor site: 3’ end has A-G dinucleotide (2 nucleotides)
    2. Branching site: Upstream of 5’ end there is sequence that is identified by A
67
Q

Describe makign of ploy(A)tail

A

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

68
Q

What does adaptor do?

A

Reads a triplet and is complimentary to it 1

69
Q

What are the termination codons?

A

UAG, UGA and UAA- nonsense codons

70
Q

What is the initiaiton codon

A

AUG

71
Q

what are the 2 AA that only have 1 codon

A

Met and Trp

72
Q

How does genetic code differs in mitochondria?

A

UGA encodes for Trp instead of stop

AAG and AGA encodes for stop instead of arginine

73
Q

tRNa have __ on 3’ end- expand on this

A

tRNa have CCA on 3’ end
Added at post-translation modification
Attachment point for AA

74
Q

Descrieb aminoacetylation of tRNA

A

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

75
Q

Initiation of translation in eukaryotes

A
  1. 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
  2. mRNA is brought in by elF4F. mRNA attachement to preinitiaiton complex requires energy
  3. mRNA is scanned until AUG codon is reached, startign from 5’ cap
  4. Large 60s subunit comes in
76
Q

Describe peptide bond formation

A
  1. Initiation Met is transferred from its tRNA to the amino group of the second AA in the A site
  2. Now there’s a dipeptidyl tRNA in the A site and unchraged tRNA in the P site
  3. Peptidyl transferase catalyses peptide bond formation
    tRNA at A site is pushed to P site
77
Q

Which factor helps in peptide bond formation?

A

Elongation factor P (EF-P)

78
Q

Factor participating in translocation

A

EF-G-GTP pushes dipeptidyl-tRNA to P site. A site becomes available

79
Q

Describe termination in translation

A

Occurs when nonsence codon arrives at A site

Release factors bind to A site releasing newly made peptide from P site

80
Q

Name release factors

A

RF1, RF2 and RF3

81
Q

What is RRF?

A

Ribosomal recycle factor- uses elongation factors and energy to dissaccosiate transaltional machinery

82
Q

Role of IF3

A

Remains attached to small subunit

Helps to reuse translational machinery

83
Q

Protein degradation

A

Attachement of Ubiquitin to lysine

E1-> E2->E3-> lysine

BC 2- (19 decks)

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