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Bioc 406 > Amino Acid Metabolism: Protein Degradation > Flashcards

Amino Acid Metabolism: Protein Degradation Flashcards

1
Q

3 ways to breakdown protein and amino acids

A
  1. Lysosomes
  2. Digestive enzymes
  3. Ubiquitin/Proteasome
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2
Q

Properties of protein, kcal, how its regulated and syntheses

A

Energy Production (4 kcal/gm)
Regulation of Glucose Levels
Fatty Acid Biosynthesis
Ketone Body Synthesis

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3
Q

Digestive enzyme: Amino acids come from digestive enzyme, name four

A

Pepsinogen
Trypsin
Chymotrypsin
Carboxypeptidases

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4
Q

How are amino acids transported, in digestive enzymes

A

Sodium-dependent amino acid Symporters Transport AA across the intestinal epithelia.
Active Protease Catalytic Triad, 3 chains held it together by disulfides to protect it from harsh environments

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5
Q

Where are amino acids transported to?

A

amino acids are relatively soluble

Transported in blood to other tissues

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6
Q

Lysosomes: breakdown and recycling of cellular components. Describe ph, membrane characteristics and acidic hydorlases

A

Lysosomal Hydrolases:
Optimal activity at pH 5
Lysosomal Membrane Proteins: Most are heavily glycosylated to prevent breakdown
Transport Proteins: Protein Import and Export of Products Proteins for membrane fusion: Allow vesicles to fuse
Acidic hydrolases: Lipases, Amylases, Proteases, Nucleases
Lysomal protein pump

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7
Q

Lysosomal Substrates process

A

Degrade cellular materials
Recycle damaged organelles
Starvation response

Autophagy engulfs around proteins in intracellular

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8
Q

Ubiquitin-Proteasome System,the major protein degradation system. Try to name the major components, seven.

A

Proteasome is a macromolecular machine designed for protein degradation
Proteasome is the major route for the degradation of intracellular proteins
Protein quality control

Also has thiorse in the macromolecule!
Removal of damaged or misfolded proteins
Cell Cycle
Progression Destruction irreversible – inactivation complete Transcriptional Regulation Immune Response Surveillance for Foreign Antigens

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9
Q

How is ubiquitan similar to tied knots? Where can it be found? Length and nature?

A

It has the basic knot to which it is an ubiquitan subunit.
Ub - 76 residue protein (8.5 kDa)
Found only in eukaryotes
Very Highly Conserved
Covalently attached to proteins including other Ubn’s to build a poly-Ub chain

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10
Q

What is Ubiquitylation of a Protein?

A

Communicates a change in Protein Location, Conformation, Activity, Binding partners, or Stability

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11
Q

How is ubiquitin more than protein degradation?

A

It has numerous signals.

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12
Q

K 63

A

Target damage DNA

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13
Q

K 11 linked

A

Target cell cycle

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14
Q

K 48

A

Target protein degradation

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15
Q

Two ways AMPK is regulated

A
  1. activity is allosterically regulated by AMP levels and phosphorylation.
  2. AMPK enzyme levels are also regulated by Ubiquitylation
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16
Q

Ubiquitylation does..

A 
Protein Conformation 
Ligand Binding 
Enzyme Activity 
Protein-Protein Interactions 
Cellular Location  
Protein Stability/Lifetime

Overall changes the landscape of proteins

17
Q

Phosphorylation does..

A

Protein Conformation
Ligand Binding
Enzyme Activity (Activates AMPK)
Protein-Protein Interactions

18
Q

Draw Ubiquitin-Transfer Pathways please

A

:)

19
Q

E1: Ubiquitin Activating Enzyme

A

•First forms a Ubiquitin-AMP intermediate with release of PPi •Then a covalent E1~Ubiquitin thioester

20
Q

E2: Ubiquitin Conjugating Enzyme

A

•Carries activated Ubiquitin as a covalent thioester conjugate •Share a conserved core domain of ~150 amino acid residues

21
Q

E3: Ubiquitin Ligase

A
  • Catalyzes the transfer of Ubiquitin to a Lys residue on a target protein
  • Humans have more E3 Ubiquitin ligases than Kinases
22
Q

How does Deubiquitinases (DUBs) catalyze the removal of Ub

A

Ubiquitin E3 ligase –covalently modifies proteins with Ub

Deubiquitinase – hydrolyzes isoamide bond between Ub and a target protein, or between linked Ub subunits

Human Genome ~ 100 DUBs

23
Q

How long does ub has to be in order to be broken down by k 48?

A

Ub chain needs to have at least 4 Ub subunits
chains can grow much longer

Rate of Protein Degradation by the Proteasome is quicker in shorter ub chains

24
Q

Three parts of Ubiquitin-Proteasome System

A

19S Particle: Composed of a Lid and a Base
20S proteasome
b-subunits are THR proteases with 3-different specificities

25
Q

Describe 19S Particle: Composed of a Lid and a Base

A

Base: ATPase subunits responsible for protein unfolding and a-Ring channel opening
Lid: Help remove Ub from captured substrates

26
Q

20S proteasome

A

stacking of 4 heptameric rings inner b-rings form the proteolytic chamber outer a-rings form an entry gate

27
Q

b-subunits are THR proteases with 3-different specificities:

A

cleave on carboxyl side of acidic, basic, or hydrophobic residues

28
Q

Mechanism of Proteasomal Protein Degradation (4 steps)

A

Recognize, unfold, and digest proteins (green) - requires ATP

Recognition signal is a Poly-Ubiquitin Chain (orange)
Ubiquitin is not degraded but is released and recycled
Present in nucleus and cytosol (free and attached to ER

29
Q

How cells let the immune system know they have been invaded by a foreign pathogen in Major Histocompatibility Complex (MHC) class I antigen presentation pathway

A

Pathogens produce proteins that get destroyed by the proteasome. The peptides are displayed on the cell surface bound to the MHC

30
Q

What is Ubiquitin Like Proteins (Ubls)

A

Post-translational modification of Proteins with Proteins

Ubiquitin and Ubls share a b-grasp fold topology

Each Ubl has its own dedicated E1, E2, and E3 system

31
Q

Ubl: Atg8 (& Atg12)

A

Essential for growth and expansion of autophagosome membranes

32
Q

Ubl: SUMO (small-Ub-related modifier) Protein interactions:

A

Nuclear transport, transcription, DNA repair, and more

33
Q

Nedd8

A

Covalent activator of Cullen Ubiquitin E3 Ligases

34
Q

Autophagy

A

Breakdown and Recycling of Cellular Components Cytoplasmic components are sequestered in autophagosomes and recycled via the lysosomal pathway

35
Q

What Induces Autophagy

A 
Starvation 
Energy 
Depletion 
Stress 
Infection 
Bacterial 
Toxins 
HIV
36
Q

How to Inhibit Autophagy

A

Nutrient
Abundance
Insulin
Microbial Virulence Factors

37
Q

Autophagy: Process of Self-Cannibalization

A

Cells capture their own cytoplasm and organelles Breakdown products are input into cellular metabolism
Energy
New proteins or membranes
Replace outdated or damaged cellular components

Starvation: provides an internal source of nutrients
Survival
Only mechanism to degrade large cellular structures
Ubiquitin signaling and Autophagy are closely linked

38
Q

Ubiquitin modification is a key…

A

signal for targeting proteins, organelles, or even invading microbes for autophagic destruction

Bioc 406 (4 decks)

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