Chapter 3 - Proteins Flashcards

1
Q

Most common regulatory small molecule added to amino acids

A

Phosphate - phosphorylation

1/3 of 10,000 or more mammalian proteins are phosphorylated at some point in time.

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2
Q

Three ways phosphorylation affects proteins

A

1) because phosphate groups carry two negative charges - can cause major conformational changes in protein structure by, for example, attracting a cluster of positively charged amino acids.
2) addition of a phosphate group can mask a binding site that otherwise holds two proteins together - disrupts protein-protein interaction.
3) attached phosphate can form part of a structure used for protein recognition. Binding sites of other proteins would recognize such structure.

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3
Q

Reversible protein phosphorylation controls the…

A

Activity, structure and cellular localizations of both enzymes and other proteins in eukaryotic cells.

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4
Q

Protein kinase catalyze what reaction?

A

Protein kinases catalyze protein phosphorylation

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5
Q

What protein remove phosphates from proteins?

A

Protein phosphatase

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6
Q

About how many amino acids are there on the average protein kinase?

A

290 amino acids

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7
Q

What are the short amino acid inserted into loops with protein kinase for?

A

Helps in recognizing the specific protein to phosphorylate.

To bind to structures that localize it in specific regions of the cell.

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8
Q

What sub family of protein kinase cause Sarcoma cancer when deregulates?

A

Src. family of protein kinases - first kind of tyrosine kinases found and strangely branched of to tyrosine kinase from an ancestral serine/threonine kinase

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9
Q

What anchors src proteins and their relatives to the cytoplasmic face of the plasma membrane?

A

A short N-terminal region that becomes covalent let linked to a strongly hydrophobic fatty acid

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10
Q

Turning on a src protein

A

Two specific things:

  1. Removal of C-terminal phosphate
  2. Binding of the SH3 domain by a specific binding protein
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11
Q

Src family protein general domains

A

NH2 - SH3 - SH2 - kinase domaine - COOH (500 amino acids)

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12
Q

GTP-binding proteins

A

Proteins regulated by binding to a GTP/GDP. Usually active with GTP form and inactive with GDP.

  • known also as GTPase because hydrolyze GTP to GDP
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13
Q

Ras protein important for

A

In cell signaling. It’s GTP-bound form, it is active and stimulates a cascade of protein phosphorylation.

Usually in inactive GDP form

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14
Q

What inactivates GTP-binding proteins?

What activates?

A
  1. GTPase-activating protein (GAP). Switches GTP to GDP.

2. guanine nucleotide exchange factor (GEF)

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15
Q

Prominent functions of phosphate and what amino acid it binds to.

A

Ser, Thr, Tyr

Drives the assembly of a protein into larger complexes

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16
Q

Prominent functions of methyl and what amino acid it binds to.

A

Lys

Helps create distinct regions in chromatin through forming either mono-, di-, or trimethyl lysine in histones

17
Q

Prominent functions of acetyl and what amino acid it binds to.

A

Lys

Helps activate genes in chromatin by modifying histones

18
Q

Prominent functions of palmityl group and what amino acid it binds to.

A

Cys

Drives protein association with membranes

19
Q

Prominent functions of N-acetylglucosamine and what amino acid it binds to.

A

Ser, Thr

Controls enzyme activity and gene expression in glucose and homeostasis

20
Q

Ubiquitin

A

Binds to Lys (48)

Monoubiquitin addition regulates the transport of membrane proteins in vesicles

Polyubiquitin chain targets protein for destruction

21
Q

Two forms of protein regulation

A
  1. Reversible binding of other molecules with protein

2. Covalent addition of small molecules to one or many amino acids in a protein.

22
Q

Two major intracellular signaling mechanisms in eukaryotes

A
  1. Signaling by phosphorylated protein

2. Signaling by GTP-binding protein

23
Q

How is ubiquitin activated?

A

Ubiquitin-activating enzyme (E1) uses ATP hydrolysis to attach ubiquitin to itself through a high energy covalent bond (thioester bond).

24
Q

Ubiquitination

A

After ubiquitin activated (attached to E1)

  1. E1 binds to ubiquitin-conjugating enzyme (E2)
  2. E2 is primed with ubiquitin (transferred from E1) and E1 released.
  3. E2 binds to ubiquitin ligase (E3)
  4. E2-E3 complex finds degradation signal on target protein and binds
  5. First ubiquitin chain added
  6. Cycles more rounds depending on purpose
25
Q

Monoubiquitylation

A

Histone regulation

26
Q

Multiubiquitylation

A

Endocytosis

27
Q

Polyubiquitylation

A
  1. Lys48 - proteasomal degredation.

2. Lys63 - DNA repair

28
Q

SUMO

A

Proteins similar to ubiquitin

29
Q

Degrons

A

Degradation signals

30
Q

SCF ubiquitin ligase description

A
  1. Adds polyubiquitin
  2. C-shaped structure formed from five protein subunits
  3. Largest subunit serves as scaffold on which the rest of the complex is built
  4. At on end of C is E2
  5. Other end is substrate binding arm (known as F-box protein).
31
Q

Rapid destruction

A

During certain cases, depending on degron, a rapid addition of multiple ubiquitin can be added. If not rapid degron, ubiquitin is added one at a time slowly

32
Q

Successful protein and evolution

A
  1. Genetic information tends to duplicate to produce a family of related proteins.
  2. Many different F-box proteins
  3. Family of scaffold as well