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NPB110A > Midterm 2 > Flashcards

Midterm 2 Flashcards

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1
Q

Central Dogma of Molecular Biology

A

DNA -> RNA -> tRNA, sRNA, mRNA -> proteins

DNA: double stranded, very stable, genetic info
RNA: single stranded, less stable
Note: all ribosomes bind their mRNA in cytosol -> can go to the ER or stay in cytosol.

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2
Q

Proteins

A

macromolecules; polymers of amino acids

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3
Q

Primary structure

A

combine amino acids through covalent bonds//sequence of AA

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4
Q

Secondary Structure

A

AA are joined by H bonds to form secondary structures

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5
Q

Function of a protein depends on..

A

Depends on its 3D conformation

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6
Q

Quaternary Structure

A

combination of several polypeptides into one structure required for function

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7
Q

ER: signal recognition particle (SRP)

A

protein that recognizes the sequence .

  • cytosolic ribonucleoprotein particle
  • it binds the large ribosomal subunit and the ER signal sequence -> Targets
  • upon binding, it stops translation
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8
Q

Translocants

A

protein that transports a protein into an organelle.

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9
Q

Translocation

A

process of transporting a protein across the cell membrane.

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10
Q

Co-translational translocation

A

The protein is transported through the membrane as it is being made.

The ribosome that is synthesizing the protein is attached directly to the ER membrane, enabling one end of the protein to be translocated into the ER while the rest of the polypeptide chain is being assem- bled. These membrane-bound ribosomes coat the surface of the ER, creating regions termed rough endoplasmic reticulum, or rough ER

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11
Q

Post-translational translocation

A

By contrast to co-translational translocation, ribosomes complete the synthesis of a protein and release it prior to post-translational translocation.

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12
Q

Sorting signals

A

Sequence of AA

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13
Q

Signal sequences or Signal Peptides

A

specific amino acid sequence of the protein

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14
Q

Translocators

A

multi-proteins (3 or 4 together)

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15
Q

Proteins without a signal

A

In the absence of any signal sequence, proteins are translated in the cytosol and then fold and remain there.

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16
Q

Translation

A

synthesis of proteins

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17
Q

ER signal sequence

A

stops translation until you reach ER

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18
Q

SRP Receptor

A

located in the ER membrane

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19
Q

How are proteins directed to the RER?

A
  1. Translation exposes signal sequence
  2. SRP binds and arrests translation (stops protein synthesis)
  3. SRP docks the ribosome nascent chain complex at the ER. Interaction between signal sequence and channel stabilizes ribosome.
  4. Translocation begins. Signal peptide is cleaved off. Nascent chain is modified and folded. Translation finishes, channel closes, and ribosome dissociates.
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20
Q

What happens when a protein enters the lumen of the ER?

A

It cannot be a membrane protein.

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21
Q

Topogenic sequences

A

Direct the membrane insertion and orientation of various classes of integral proteins.

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22
Q

Transmembrane sequence

A

stop transfer anchor sequence

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23
Q

Topology

A

Refers to the number of times that its polypeptide chain spans the membrane and the orientation of the segments in the membrane.

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24
Q

Sorting of Proteins to Mitochondria

A

Protein needs to be unfolded to go through mitochondria and stays unfolded because of chaperones.
- Completely synthesized protein in cytosol. -> matrix target signal

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25
TOM
translocon of outer membrane
26
TIM
translocon of inner membrane
27
Energy for movement
- For Chaperones: (proteins that help fold/unfold other proteins); in the cytosol and in the matrix need ATP - Charge/pH gradient that exists across the inner mitochondrial membrane -> ELECTROMOTIVE FORCE -> used to make ATP
28
Endocytic Pathway
comprises of early and late endosomes and lysosomes (plasma membrane -> lysosome)
29
Exocytic Pathway
comprises of the endoplasmic reticulum (including the nuclear envelope) and the Golgi apparatus (endoplasmic -> plasma membrane)
30
Coated vesicles
used to carry materials between compartments
31
2 distinct functions of protein coats
1. cause the membrane to curve and form a vesicle | 2. select the components to be carried by the vesicle
32
COPII-coated vesicle
move materials from the ER "forward" to the Golgi complex
33
COPI-coated vesicle
move materials from Golgi "backward" to ER, or from the trans Golgi to the cis Golgi cisternae
34
Clathrin-coated vesicles
move materials from the plasma membrane to endosomes, lysosomes, and plant vacuoles
35
Primary mechanism by which the vesicle coat selects proteins
The primary mechanism by which the vesicle coat selects proteins is by directly binding to specific sequences or sorting signals in the cytosolic portion of the membrane cargo proteins.
36
Luminal sorting signal
bind the luminal domains of certain cargo proteins
37
Cargo receptor protein
linking protein to indirectly bind a coat protein to cargo (if the cargo is a soluble protein)
38
Anterograde Transport
(ER --> Golgi) by the COPII vesicles
39
Retrograde transport
(Golgi --> ER) by the COPI vesicles - Important for retrieving transport proteins, membrane, etc. - Also returns mis-sorted proteins to the ER - Mutations in the COPI proteins not only stops retrograde transport but, in time, also stops all anterograde transport, as the ER is depleted of proteins and membrane necessary for sorting
40
KDEL signal sequence and protein trafficking
Most soluble ER-resident proteins carry a Lys-Asp-Glu-Leu sequence at their C-terminus (KDEL) This signal is sufficient and necessary for sorting proteins to the ER - Adding it to a normally secreted protein causes it to be sequestered to the ER - Removing it from an ER-destined protein results in it being secreted The KDEL receptor is located in vesicles between ER and Golgi. Their binding to proteins is pH dependent. KDEL signal brings the protein back once they escape the ER, preventing them from leaving the ER --> serves as an "ER-retention" signal In the Golgi, there is a more acidic pH --> receptor can recognize KDEL and binds it --> causes protein to travel back to ER --> pH in ER is different (more basic) --> KDEL and protein separate These proteins are supposed to be kept in the ER - Recognition in the Golgi brings the protein back to the ER
41
Golgi Complex
The Golgi complex is organized into 3-4 subcompartments. Each subcompartment has different enzymes, many of which are glyceridases and glycosiltransferases.
42
Cisternae Maturation Model
Vesicles of protein secreted by ER merge with vesicle of enzymes from old cis to form new cis enzymes from old medial merge with old cis to form new medial same shit for medial--> new trans old trans become vesicles secreted to membrane How was this discovered? Bound early Golgi proteins to GFP(green) and late GOlgi proteins to dsRED(Red) and placed them into a vesicles, then tracked vesicle over time. Vesicle started out with just green, then turns red over time. This means red protein gets added over time while green proteins being taken out and sent to next vesicle
43
Mislocalized proteins
proteins associated with disease
44
GCPRs
- Involved in a wide variety of signaling. - All have a similar structure: single polypeptide chain; crosses the membrane 7 times ("serpentine receptors") - similar proteins can be found in bacteria(so evolutionary ancient), though they do not act through G-proteins
45
Signal Transduction
done by G-protein-coupled receptors. - ligand binding on the extracellular domain changes the intracellular domain - affinity for G-proteins increases and the receptors binds a G protein intracellularly - GDP is exchanged for GTP on the G-protein, activating the G-protein - one ligand-bound receptor can activate many G proteins
46
Levels of cAMP if increased AC, decreased PDE
Increased cAMP
47
Levels of cAMP if decreased AC, increased PDE
very little cAMP
48
Protein kinase A
activated when cAMP binds to its regulatory (inhibitory) subunit
49
ADP Ribosylation
inactivates proteins
50
Mono-ADP-ribosylation
enzymatic transfer of ADP-ribose from NAD+ to acceptor proteins
51
Normal Gs
GTPase activity terminates the signal from receptor to adenylyl cyclase
52
ADP-ribosylated Gs
GTPase activity is inactivated; Gs constantly activates adenylyl cyclase
53
Cholera
infection of the small intestine that is caused by the bacterium Vibrio Cholerae
54
Cholera Toxin
enzyme that catalyzes the transfer of ADP ribose from intracellular NAD+ to the alpha subunit of Gs
55
Pertussis toxin (PT)
protein-based toxin produced by the bacterium Bordetella pertussis which causes whooping cough, catalyzes the ADP ribosylation of the alpha-subunit of Gi.
56
Calmodulin
2 heads -> calcium binding domains
57
CaM-Kinase
activated by calcium. binding of Ca2+ to Calmodulin induces a conformational change that enables it to wrap around a target protein.
58
intracellular domain
either acts as an enzyme or forms a complex with another protein that acts as an enzyme
59
Enzyme Coupled Receptors
- transmembrane proteins - contain an extracellular ligand binding domain - usually one transmembrane domain (so poor chance of ligand-induced conformational changes)
60
Receptor Tyrosine Kinases
- binding of the ligand induces the dimerization of the receptor subunits - contact between the intracellular tails result in their activation and cross-phosphorylation
61
SH2 domain
binds phosphorylated tyrosin
62
Protein Scaffolds
protein that you can add other proteins to bring them together
63
Tyrosine Phosphatases
removes phosphate group
64
Termination of a signal
Phosphates are removed by protein tyrosine phosphatases in response to extracellular signaling or by endocytosis and degradation.
65
Traditional Nuclear Signaling Pathway
- it sometimes works as a single receptor, sometimes as a dimer - act on transcription factors affecting gene expression
66
Ligand
hydrophobic; ligand finds a receptor that can be in: cytosol or nucleus
67
Receptors
Can be located in the membrane or in the cytosol. They affect many aspects of cell function: division, differentiation, expression levels of receptors, etc. They act by modulating gene transcription by altering chromatin structure or turn transcription factors on or off.
68
MAP kinase pathways
MAP: mitogen activation protein
69
RAS proteins
it is a family of small GTP-binding protein (monomer G proteins) that have GTPase activity, are bound by a lipid tail to the cytoplasmic tail of the plasma membrane. - Almost all RTKs activate a RAS protein
70
Necrosis
- cellular swelling - membranes are broken (water enters, cell swells and explodes) - ATP is depleted - Cell lyses, eliciting an inflammatory reaction - DNA fragmentation is random, or smeared - in vivo, whole areas of the tissue are affected
71
Apoptosis
- cellular condensation - membranes remain intact - requires ATP - cell is phagocytosed, no tissue reaction - ladder-like DNA fragmentation - in vivo, individual cells appear affected
72
Cytochrome C
component of ETC to transport electrons to generate gradient; it is an inner mitochondrial membrane protein
73
Histones
DNA wrapped around the histones make a nucleosome
74
endonuclease
cut dna in between nucleosomes
75
Intrinsic Pathway (Suicide Pathway)
an intracellular signaling cascade that is set in motion when not enough survival factors are detected by a cell.
76
Caspase
Caspase stands for: Cytesine residue in their catalytic site and selectively cleave proteins at sites just C-terminal to Aspartae residues. They work as homodimers.
77
Zymogens
Nonactive form of enzymes.
78
Bcl-2
Like CED-9, is an anti-apoptotic factor. Prevents the activation of Apaf-1.
79
Bax
can form oligomeric channels that allow for ion flux, somehow this causes the release of Cyt C from mitochondria and triggers apoptosis.
80
Death signals
Promote apoptosis (TNF, Fas ligand) to kill bad cells.
81
TNF
part of the immune and inflammatory response
82
Fas ligand
leads to cell death in virus infected cells and tumor cells
83
Death receptors
receptors for TNF and Fas ligand
84
TBADD
adaptor protein that recognizes death receptor to recruit FADD (Fas associated death domain)
85
FADD (Fas associated death domain)
recruits and somehow activates Procaspase-8
86
Caspase-8
initiator caspase; activates other caspases leading to an amplification cascade that causes apoptosis.

NPB110A (1 decks)

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