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Bcem 431 > Lecture 9 > Flashcards

Lecture 9 Flashcards

1
Q

When is protein kinase c active

A

When it’s bound to the membrane and has calcium and DAG bound

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2
Q

what is the C2 region of protein kinase c made of an how does it help

A

It’s has a poly basic cluster of lysine residues that are postively charged

These lysine residues help it bind to the membranes negative charged phosphotidyl serine lipid heads

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3
Q

C1 and C2 domains of PKC binds what

A

C1A and C1B binds DAG

C2 binds the Phosphatidylserine and Phosphotidyl inositol lipid head groups (so the PIP2 groups) and calcium

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4
Q

To activate protein kinase C what domains have to be bound

A

The C1A or C1B (only need one bound to dAG to activate it)

The c2 to the membrane (Phosserine and PIP2)

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5
Q

What motif is in the c1 domains of PKC

A

The zinc finger motif

So it has two zinc ion (one in a and one in B)

Surrounded by 3 cysteine and 1 his each

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6
Q

What are the steps of PKC getting activated

A

DAG and ca are required

When ca, PKC goes to membrane, C2 domain binds pip2 and phosserine head groups

C1A or B bind DAG and the autoinhibitory site on PKC comes out (off)

The PKC is now active

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7
Q

What are the steps of PKC getting activated

A

DAG and ca are required

When ca, PKC goes to membrane, C2 domain binds pip2 and phosserine head groups

C1A or B bind DAG and the autoinhibitory site on PKC comes out (off)

The PKC is now active to activate other proteins involved in growth (because the kinase what activated by a growth factor)

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8
Q

What does PLC do

A

Once a GPCR is activated by a growth factor or other signal, the PLC is activated and cleaves PIP2 into DAG and IP3

This DAG binds to C1A of PKC to activate it

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9
Q

Why is magnesium in high concentrations in the cell (mM)

A

Because it is always bound to atp so it can stabilize the negative phosphate charge in atp

The amount of ato in the cell is also high, to mg would also have to be high

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10
Q

Is there free atp in cells

A

No since mg is always bound, mg-ATP is mostly what there is

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11
Q

To what phosphates is the mg in atp bound to

A

The beta (2nd) and gamma (3rd) phosphates

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12
Q

What is the coordination of mg when bound to the phosphates of atp

What does the mg bind to

A

Mg2+ so hard metal surrounded by oxygens, typically from water

octahedral geometry

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13
Q

Where else if magnesium found

A

In chrlorophyll

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14
Q

If magnesium isn’t bound to chlorophyll what happens

A

The absorbance of light from the sun changes, so red and blue light isn’t absorbed

It needs to absorb red and blue light for photosynthesis to happen and to make oxygen

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15
Q

Chlorophylls are a type of

A

Porphoryn (like hemoglobin)

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16
Q

Know how to draw general structure of chlorophyll

A

Slide 6

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17
Q

What is the exception of mg in chlorophyll and why

A

Mg2+ is a hard metal so it should bind to oxygen, but in chlorophyll it binds to nitrogen

This is because of the delocalized structure and electrons of chlorophyll surrounding it

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18
Q

What are the types of PTM in proteins

A

Phosphorylation

Ubiquitinations

Glycosylation

Methylation

Acetylation

Sumoylation

Sulfurylation

Fatty acylation (lipidation)

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19
Q

What do PTMS do

What is the evidence

A

they add groups to proteins to alter their function

When purified, proteins have modified amino acids (phosposerine, dimethylargenine)

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20
Q

What do PTMS do

What is the evidence

A

they add groups to proteins to alter their function

When purified, proteins have modified amino acids (phosposerine, dimethylargenine)

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21
Q

When can PTM happen

A

Cotranslationally (during translation)

Posttranslationally (after translation)

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22
Q

Are PTM specific or not

A

Yes specific, needs dedicated enzymes to doing the modification

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23
Q

Where to PTMS usually happen

How do they happen somewhere else

A

Usually on the surface of proteins

But if the modification is done cotranslationally and the protein folds, it can become internal

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24
Q

Are PTMS reversible

A

Yes

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25
Q

What are most PTMS triggered to happen by

A

Receptors on the cell surface (like GPCR receptors)

Like a singal for the cell to grow or kill itself makes the according PTM happen to do this

26
Q

What is an example of a cotranslational modification

What does it help with

A

Disulphide bond formation (in extracellular proteins)

They form spontaneously and restrict the motion of previously flexible part of the protein

This limits proteolytic digestion

27
Q

What an example of a protein with disulphide bonds

What type of protein is it

A

Bovine pancreatic trypsin inhibitor (BPTI)

It’s a toxic protein, toxic proteins usually have three disulphide bonds

28
Q

If dipulphide binds aren’t present what happens to the structure of the protein

A

Structure Changes drastically

This is why disulphide bonds are really important to structure

29
Q

What is hydroxyproline

What can it do

A

A modified proline (has extra OH on corner of ring)

Forms extra h bonds compared to just proline

30
Q

What is hydroxyproline found in and what can it help with

A

It’s found in collagen, and thought the extra h binds it can make it stabilizes the strands of collagen

Required enzymes to do and vitamin c

31
Q

What is gamma glutamayl carboxylase

A

An enzyme that adds an extra carboxyl group on the gama carbon of glutamate

This to makes gamma carboxy glutamic acid (Gla)

32
Q

What is Gla used for

A

The extra negative charge from the extra gamma carboxy is used to coordinate calcium.

The now two coo- coordinate ca to create a membrane binding motif for the protein that Gla is in (to make the protein bind to the membrane)

Also heavily involved in the process of blood clotting (so enzymatic reactions

33
Q

What is amino acid is a common target for sulfurylation

What enzyme does this

Where does it happen

A

Tyrosine

Sulfotransferase

In the golgi (so only happens to proteins that are secreted from the cell)

34
Q

How does tyrosine sulphurylation happen

A

The precursor PAPS act like a sulfate donor (for many things)

Needs an OH group to transfer the sulfur (which is why tyrosine)

After transfer PAPS turns to PAP

35
Q

What is the purpose of tyrosine sulfurylation

A

To increase interactions between two proteins

Ex. The GPCR and its hormone ligand bind closer together because of surphurylation

36
Q

How is PAPS made in humans

A

Via PAPS synthase which is a bifunctional enzyme that takes both atp and sulfate in the cell and make PAPS

37
Q

How is PAPS made in plants /bacteria

A

Needs two enzymes because it doesn’t have a bifunctianal enzyme

First atp turns to APS via ATP sulfurylase (adds sulphate)

Then APS turns to PAPS through APS kinase (adds phosphate)

38
Q

What is polyubiquitin

What is ubiquitin

A

More than two ubiquitin proteins

A small 76AA protein

39
Q

What happens if poly ubiquitin is added to a protein

What if one ubiquitin

A

The protein gets targeted for degredation by the proteasome (death star)

Cant target for death, the ubiquitin is used for signalling

40
Q

What is the motif for polyubiquiting protien getting added to proteins

A

D-K-X-E

The lysine in the proteins motif is what’s targeted to get ubiquitinated

41
Q

What is the Death Star structure

A

Has 2 19S caps and a 20S core

Total protein is 26S

42
Q

How does the Death Star work

A

The 19s caps cleave the polyubiquitin and use atpases to unfold the protein

They then get the unfolded protein into the 20s core which chops up the polypeptide

The broken peptides are shot out the second 19s cap

43
Q

Where is the protease activity of the Death Star

What does the Death Star depend on

A

In the 20s core

Atp dependent (to unfold protein)

44
Q

What is normoxia and hypoxia

A

Normal levels of oxygen

Low oxygen

45
Q

How do PTMS help cells sense and adapt to oxygen availability under normoxia

A

In normoxia (oxygen rich):

the 2 prolines of HIF 1aplha get hydroxylated

VHL gets recruited to HIF1a

Then the HIF1a gets targeted for degredation (meaning ubiquitination hapoens on a lysine residue)

46
Q

How do PTMS help cells sense and adapt to oxygen availability under hypoxia

A

The hydroxylation of proline on HIF1a doesn’t happen

HIF1a goes into the nucleus and binds to ARNT to act as a transcriptional activator

Help to transcribe the HRE (hypoxia response element) genes that get more oxygen to us

47
Q

What types of things does HIF1-a help make in hypoxia conditions

A

Genes for Blood vessels (angiogenesis)

Higher metabolism (glycolysis)

Body also makes more red blood cells (erthyropoesis)

48
Q

What is sumoylation

What does it do

A

Also covalently binds to lysine (like ubiquitin, protien bind to protein)

Attachment of it to proteins changes the proteins subcellular localization, transcriptional activity, stability, protects it from degredation

49
Q

What is the motif for sumoylation

A

yKXE

y= hydrophobic amino acid (diff from ubiquitination because that one is D (hydrophilic)

X= any amino acid

50
Q

How does the sumoylation of something protect is from degredation

A

Once the protein is produced, One side of the protein is hydrophobic so it’s sticky.

Stick end Doesn’t want to be exposed , so the sumo gets added there to protect the protien from misfolding

51
Q

How does the sumoylation of something increase its stability (acceptable answer)

A

Protects the exposed area of the protein from degredation

52
Q

Give an example of What protein phosphorylation does to a protein

A

Induces conformational changes in glycogen phosphorylase

Glycogen phosphorylase releases glucose from glycogen

53
Q

What thing phosphorylated proteins

A

Proteins kinase

54
Q

How does phosphorylation help in smooth muscle contraction

A

Requires calcium Cam (so caM with calcium bound)

Needs myosin like chain kinase

Contraction happens when ca-cAM activate the MLCK

Myosin phosphorylated and contraction happens

A phosphotase would take off the P so get relaxation of smooth muscle

55
Q

What are the kinase activators in the cell and what kinase do they activate

A

Cyclic - amp (PKA)

Ca-cam (cam dependent kinase)

Cyclic gmp (PKG)

DAG (PKC)

56
Q

What are the kinase activators in the cell and what kinase do they activate

A

Cyclic - amp (PKA)

Ca-cam (cam dependent kinase)

Cyclic gmp (PKG)

DAG (PKC)

57
Q

What motif does PKA recognize

A

arg-arg-xxx-ser-Val-xxx

R-R-X-S-V-X

The serine can also be a threonine (thr)

58
Q

What motif does MAPK (proline directed kinase) recognize

A

Ser-Pro-Lys- Lys

S-P-K-K

Serine can also be threonine

59
Q

What motif does casein kinase 2 recognize

A

Ser-xxx-xxx-glu/asp

S-X-X-E/D

Serine can be threonine

Need - charge at end

60
Q

What is RYR

A

A calcium channel

Bcem 431 (26 decks)

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