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Biochem II Self Study > Lecture 16 review (exam 3) > Flashcards

Lecture 16 review (exam 3) Flashcards

1
Q

Protein (enzyme) regulation

A
  1. Protein synthesis / gene regulation
  2. Zymogen activation (targeted proteolysis)
  3. Allosteric regulation (feedback inhibition)
  4. Covalent modificaiton
  5. Cellular compartmentalization
  6. Protein-Protein interactions
  7. protein degradation
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2
Q

Six steps to control eukaryotic gene expression

A
  1. Transcriptional control
  2. RNA processing
  3. RNA transport
  4. Translational control
  5. mRNA degradation
  6. Protein processing (activity)
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3
Q

Phosphorylation

A
  • on Ser, Thr, His, Asp or Tyr residues
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4
Q

Phosphorylation is used to:

A
  • reversibly regulation protein function via conformational changes due to charges rather than size
  • enable binding events in signal transduction
  • approx. 33-50% of all proteins are phosphorylated at a given time
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5
Q

Phosphorylation regulates

A

major pathways of replication, transcription, translation, metabolic pathways, DNA repair

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6
Q

Most kinases require….

A

some type of activating event to potential their kinase activity (ex. allosteric activation)

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7
Q

Phosphorylation in mammalian cells

A

on Ser, Thr or Tyr residues
reasonably stable

charge of phosphoryl group is about 1.7

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8
Q

Phosphorylation in prokaryotic ells

A

on Ser, Thr, Asp or His residues

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9
Q

Protein kinases

A

phosphorylated using ATP as the donor

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10
Q

protein phosphatases

A

dephosphorylate, not reverse of phosphorylation

product is inorganic phosphate

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11
Q

Protein kinases/phosphatases recognize…

A

consensus sequences around the phosphorylation target site

ex. SQ/TQ context; recognized and targeted by two cell cycle checkpoint kinases, ATM + ATR

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12
Q

Phosphorylation effects on proteins

A
  • activate or inhibit enzyme activity
  • potentiate or attenuate protein-protein interactions
  • affect cellular localization
  • increase or decrease rate of protein degradation
  • affect interactions with metabolites, substrates or regulatory molecules
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13
Q

Dynamic Human kinome

A

540 known and characterized kinases

divided into 8 separate groups on basis of sequence and structure

includes Ser/Thr and Tyr kinase families

linked to 670 known human diseases

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14
Q

Phosphorylation of mammalian pyruvate dehydrogenase

A

PD phsophatase: activates PD
PD kinase: inactivates PD (allosterically regulated)

Pyruvates + NAD+ –(PD)—> Acetyl-CoA + NADH

+ADP, Ca2+
- NADH, Acetyl-CoA

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15
Q

2-component signaling Prokaryotes

A

Sensor Histidine kinase (component 1)

response receiver/regulator (comp 2) that is always phosphoaspartate

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16
Q

Component 1

A

Sensor Histidine kinase

direct phosphoryl transfer

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17
Q

Component 2

A

response receiver / regulator that is always phosphoaspartate

chemical hydrolysis ends signal

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18
Q

Autophosphorylation

A

most kinases can phosphorylate themselves

  • Auto-P can be activating or inactivating
  • generally believed to be one molecule phosphorylating another molecule rather than phosphorylating itself
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19
Q

ATM dimer auto-P

A

causes its dissociation and activation as a kinase

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20
Q

kinases will phosphorylate other kinases

A

Kinase cascades
- amplify signals
- may be linear or branched
- may be activating or inhibiting or both
- can link tyrosine kinases to serine/threonine kinases
- can move signals with a cell

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21
Q

Protein Acetylation

A

Donor: acetyl-CoA
Acceptor: commonly a lysine

Protein acetyl transferase: acetylates proteins
Protein deacetylase: deacetylates proteins

Acetylation and deacetylation of proteins occur as regulatory events

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22
Q

protein acetyl transferase

A

acetylates proteins

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23
Q

protein deacetylase

A

deacetylates proteins

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24
Q

Effects of protein acetylation

A

effects on protein strucutre-function
- inhibition of catalytic activity
- enhancement of catalytic activity
- alteration of substrate specificity
- enhancement of protein degradation
- promotino of protein-protein interactions
- enhancement of cytoplasmic localization

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25
Q

Acetylation of liver metabolic events

A
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26
Q

Protein glycosylation

A

covalent modification of a protein with a carbohydrate

mono-glycosylation, poly-glycosylation

glycosylation can occur on several amino acid side chains

27
Q

N-linked glycosylation

A

ER lumen, Asparagine

28
Q

O-linked glycosylation

A

Golgi, Threonine (or serine)

29
Q

mono-glycosylation

A

addition of O-GlcNac (intracellular proteins)

30
Q

Poly-glycosylation

A

addition off oliosaccharide chains (glycans)

(membrane proteins, secreted proteins)

31
Q

Protein glycosylation in vivo functions

A
  • glycosylation increases solubility of the protein (more H bonding possibilities)
  • glycans function as zip codes to target the protein to the correct location (receptor recognize sugars)
  • presence of complex carbohydrate side chains protects protein from proteolysis
  • glycosylation facilitates secretion of proteins
32
Q

O-GlcNAcylation functions in cellular pathways

A

transcription, translation, cell division

33
Q

O-GlcNac targets

A
  • RNA pol II
  • Nucleoporins
  • oncogenes
  • tumor supressors
  • cytoskeletal proteins
34
Q

Covalent modification by lipid as a regualtory event

A

protein acylation, protein prenylation

35
Q

Protein acylation

A

covalent modifications of amino acid side chains iwth long chain fatty acids

typical donor: palmitoyl-CoA

36
Q

protein acylation occurs on

A

Ser or Thr side chain: O-acylation

amino terminus: N-acylation

Cys side chain: Thio (or S-) acylation

37
Q

protein prenylation

A

addition of isoprenyl units to a protein

occurs on a cysteine close to the C-terminus of the protein (“CAAX”)

typical donor: pyrophosphorylated lipid

38
Q

Ubiquitination and Sumoylation

A

Covalent modifications of a small protein, ubiquitin or SUMO (small ubiquitin-like modifier) to a target protein in an isopeptide bond

39
Q

Multiple sumoylation and ubiquitination events regulate

A

a DNA replication protein

40
Q

Signal sequences - Molecular Zipcodes

A

many sorting protein sorting signals are localized in a stretch of amino acids

signal sequences can be at the protein termini or an internal strentches

41
Q

Protein transport: cytoplasm <–> nucleus

A

NPC: nuclear pore complex, consist of 30 nucleoporins

the nuclear localization signal on a protein is recognized by a nulcear import receptor

42
Q

nuclear import receptor

A

are often specialized towards a subset of “cargo proteins”

43
Q

Transmembrane transport: Protein translocation into mitochondria

A

protein translocator complexes

Depending on the localization signal on the protein, it will be integrated into a membrane or go all the way (matrix space)

44
Q

protein translocator complexes

A

protein translocation into mitochondria

mediate transport across the outer and inner mitochondrial membrane

45
Q

Transmembrane transport: peroxisomes

A

Short amino acid sequences taret proteins across the peroxisome membrane

46
Q

peroxisome

A

an oxidative organelle that participates in degradation of molecules to harvest energy

Peroxisomes produce H2O2 instead of H2O during last electron transfer step

47
Q

endoplasmatic reticulum (ER)

A

The ER has central roles in lipid and protein biosynthesis; it also serves as intracellular Ca2+ store

all secretory proteins + proteins targeted to ER lumen, Golgi or lysosomes are initially brought to the ER

48
Q

Protein transport into the endoplasmatic reticulum (ER)

A

Proteins targeted for the ER carry an ER signal sequence

SRP (signal recognition particle) binds to ER signal sequence and to the SRP receptor

The translocator inserts the signal sequence into the membrane and translocates the protein across the membrane

49
Q

Three main types of coated vesicles

A

Clathrin, COPI, COPII

50
Q

Coated vesicle: coat functions

A
  1. it molds the forming vesicle and shapes it
  2. it concentrates specific membrane proteins in one patch
51
Q

Phosphoinositides

A

mark organelles and membrane domains

  • Different organelles have distinct sets of PIP kinases and phosphatases
  • Different PIPs are located on different membranes
52
Q

Vesicle targeting

A

Rab proteins and SNARES

53
Q

Rap proteins

A

GTPases that bring vesicles to their target membrane
—>
Rab-GTP binds to Rab effector

54
Q

SNAREs

A

mediated membrane fusion

55
Q

Golgi: processing of oligosaccharides

A

Different parts of the golgi perform distinct oligosaccharide processing steps

Also in Golgi: O-linked glycosylation; Heaviest O-glycosylation occurs on mucins and proteoglycans

56
Q

Lysosomes

A

are the major site for intracellular degradation of macromolecules

contain hydrolytic enzymes that work only under acidic conditions

57
Q

Pathways that deliever to the lysosomes

A

phagocytosis
endocytosis
autophagy

58
Q

Endocytosis

A

Phagocytosis, Pinocytosis, Receptor-mediated endocytosis

59
Q

Phagocytosis

A

ingestion of large particles (microorganisms and dead cells)

60
Q

Pinocytosis

A

ingestion of fluids and solutes

61
Q

Receptor-mediated endocytosis

A

often clathrin-coated

62
Q

Exocytosis

A

constitutive secretory pathway
regulated secretory pathway

63
Q

regulated secretory pathway

A

secretory vesicles are stored just underneath the plasma membrane

they release their contents to the cell exterior by exocytosis in response to a specific signal

Biochem II Self Study (10 decks)

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