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

Lecture 16 review (exam 3) Flashcards

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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
Acetylation of liver metabolic events
26
Protein glycosylation
covalent modification of a protein with a carbohydrate mono-glycosylation, poly-glycosylation glycosylation can occur on several amino acid side chains
27
N-linked glycosylation
ER lumen, Asparagine
28
O-linked glycosylation
Golgi, Threonine (or serine)
29
mono-glycosylation
addition of O-GlcNac (intracellular proteins)
30
Poly-glycosylation
addition off oliosaccharide chains (glycans) (membrane proteins, secreted proteins)
31
Protein glycosylation in vivo functions
- 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
O-GlcNAcylation functions in cellular pathways
transcription, translation, cell division
33
O-GlcNac targets
- RNA pol II - Nucleoporins - oncogenes - tumor supressors - cytoskeletal proteins
34
Covalent modification by lipid as a regualtory event
protein acylation, protein prenylation
35
Protein acylation
covalent modifications of amino acid side chains iwth long chain fatty acids typical donor: palmitoyl-CoA
36
protein acylation occurs on
Ser or Thr side chain: O-acylation amino terminus: N-acylation Cys side chain: Thio (or S-) acylation
37
protein prenylation
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
Ubiquitination and Sumoylation
Covalent modifications of a small protein, ubiquitin or SUMO (small ubiquitin-like modifier) to a target protein in an isopeptide bond
39
Multiple sumoylation and ubiquitination events regulate
a DNA replication protein
40
Signal sequences - Molecular Zipcodes
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
Protein transport: cytoplasm <--> nucleus
NPC: nuclear pore complex, consist of 30 nucleoporins the nuclear localization signal on a protein is recognized by a nulcear import receptor
42
nuclear import receptor
are often specialized towards a subset of "cargo proteins"
43
Transmembrane transport: Protein translocation into mitochondria
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
protein translocator complexes
protein translocation into mitochondria mediate transport across the outer and inner mitochondrial membrane
45
Transmembrane transport: peroxisomes
Short amino acid sequences taret proteins across the peroxisome membrane
46
peroxisome
an oxidative organelle that participates in degradation of molecules to harvest energy Peroxisomes produce H2O2 instead of H2O during last electron transfer step
47
endoplasmatic reticulum (ER)
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
Protein transport into the endoplasmatic reticulum (ER)
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
Three main types of coated vesicles
Clathrin, COPI, COPII
50
Coated vesicle: coat functions
1. it molds the forming vesicle and shapes it 2. it concentrates specific membrane proteins in one patch
51
Phosphoinositides
mark organelles and membrane domains - Different organelles have distinct sets of PIP kinases and phosphatases - Different PIPs are located on different membranes
52
Vesicle targeting
Rab proteins and SNARES
53
Rap proteins
GTPases that bring vesicles to their target membrane ---> Rab-GTP binds to Rab effector
54
SNAREs
mediated membrane fusion
55
Golgi: processing of oligosaccharides
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
Lysosomes
are the major site for intracellular degradation of macromolecules contain hydrolytic enzymes that work only under acidic conditions
57
Pathways that deliever to the lysosomes
phagocytosis endocytosis autophagy
58
Endocytosis
Phagocytosis, Pinocytosis, Receptor-mediated endocytosis
59
Phagocytosis
ingestion of large particles (microorganisms and dead cells)
60
Pinocytosis
ingestion of fluids and solutes
61
Receptor-mediated endocytosis
often clathrin-coated
62
Exocytosis
constitutive secretory pathway regulated secretory pathway
63
regulated secretory pathway
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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