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PSU Freshman > BIOL230W Exam 2 > Flashcards

BIOL230W Exam 2 Flashcards

Weeks 4-6

1
Q

Where does the CFTR protein localize?

A

Plasma membrane to help regulate water concentration in mucus

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2
Q

Where do proteins function in the cell?

A

Cytoplasm, endosymbiotic organelles, ER

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3
Q

Which organelle will “read” the information in the mRNA and convert it to a protein sequence?

A

Ribosome

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4
Q

Where in the cell is the ribosome located at the start of translation? What two locations can translation be terminated?

A

Cytoplasm, ends in cytoplasm or ER

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5
Q

The translocon allows passage between which two areas of the cell?

A

ER lumen and cytosol

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6
Q

If the signal peptide of a new protein directs the ribosome to the translocon, would it need to be translated first or last?

A

First so it can finish translation in the ER
-Proteins destined for membranes or export from the cell finish translation into the ER lumen –>cotransational translation

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7
Q

If translated through the translocon, where would the proteins ultimate destination?

A

endosome

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8
Q

5’ mRNA codes for a signal peptide, then (Protein translation steps)

A

the SRP binds the signal peptide of the N-terminus of the new protein
2) SRP facilitates binding of the ribosome to a translocon
3)Protein translation finishes in the ER and the protein must be correctly folded for subsequent packaging into a transport vesicle

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9
Q

What characteristic do amino acids have that span the hydrophobic core of a membrane share?

A

Hydrophobic/nonpolar

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10
Q

What monomers make up a protein polymer?

A

amino acids

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11
Q

What makes one amino acid different from another?

A

differing side chains (nonpolar, charge, polar)

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12
Q

What is the name of the bond that connects monomers into the polymer?

A

Covalent bonds

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13
Q

How is a polypeptide analogous to a molecule of DNA or mRNA? How are they different?

A

They are polymers made of monomers with backbones and polarity. DNA is composed on nucleotides with 3’ ends and 5’ ends. mRNA is made of amino acids with N/C terminus’

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14
Q

What molecule do all G-proteins bind to and eventually hydrolyze?

A

GTP (guanine triphosphate)

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15
Q

G-proteins are active when bound to what molecule?

A

Activated by G protein-coupled receptors
stimulate GTP binding

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16
Q

G-proteins are inactive when bound to what molecule?

A

GDP
inactivated by RGS proteins b/c stimulate GTP hydrolysis

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17
Q

RNA molecules that catalyze reactions are called

A

ribozyme

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18
Q

Why are ribosomes classified as ribozymes?

A

They add amino acids together with polypeptide bonds (catalyze)
- enyzme function

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19
Q

Transfer RNA is a

A

single strand RNA that has a secondary structure mediated by hydrogen bonds between hydrogenous bases
-contains anticodon region, AA binding region
-AA is covalently attached by amino t RNA synthase

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20
Q

Process of translation includes (3 steps)

A

1) tRNA
2) G-proteins
3)Ribosome

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21
Q

Proteins that function in a membrane area are anchored by…

A

hydrophobic amino acids

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22
Q

As a membrane protein is translated through the translocon, a stretch of hydrophobic AA’s interact with

A

the hydrophobic core of lipid bilayer

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23
Q

What is the name and function of the G-protein in this step of elongation?

A

GTP, brings charged tRNA to A site

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24
Q

The tRNA’s anticodon binds to the mRNA codons to

A

synthesize the protein. The genetic code is redundant: multiple codons for one amino acid

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25
Describe the covalent bond that is formed and the bond that is broken by the peptidyl transferase center of the ribosome?
The peptidyl transferase center of the ribosome forms a peptide bond between the amino acid the P site and growing polypeptide chain in the A site. The ester bond between the tRNA in the P site and the growing polypeptide chain is broken
26
Compare and contrast the ribozyme with the other non-coding RNA's
Ribozyme forms the peptide bond enzymatically -catalyzes the formation of peptide bonds ' Other non-coding RNA are sequence-specific guides (tRNA, mRNA, sRNA) - do not catalyze a reaction -tRNA uses sequence specific structure to transport AA's
27
How many nucleotides does the ribosome move during translocation?
3 nucleotides along the mRNA molecule
28
What is the name of the G-protein that function in this event?
GTP-binding elongation factor (G (EF-G) is the G protein involved. EF-G facilities the movement of the ribosome along the mRNA during translocation by hydrolyzing GTP
29
Termination occurs
when a stop codon is encountered
30
Termination has a release factor that binds to
codon in A site, which triggers hydrolysis of GTP, new peptide chain released. After hydrolysis, the ribosome complex dissociates
31
Hierarchy of protein structure
Primary -AA structure Secondary -H bonds of backbone Tertiary -Interactions between R groups Quaternary -Multiple subunits
32
Secondary structure has
alpha helices and beta sheets and is stabilized by backbone
33
Super secondary structure occurs when
2-4 secondary structures interact
34
Tertiary structure is mediated by
H-bonds, disulfide bonds (covalent) and/or hydrophobic reactions
35
A protein domain is a part of protein that can
evolve, function and exist independent of the rest of the protein
36
Domains dictate the
functionality of the protein
37
A structural motif is a functional part of a protein defines by
super secondary structure -cannot function without the rest of the protein
38
What are the 3 main destinations of translated proteins?
Cytoplasm, endosymbiotic organelles or nucleus(transport of proteins after translation0, and endomembrane system
39
What macromolecule can be post-translationally added to a protein, so it localizes to the inner (or outer leaflet) of the cell membrane? Why?
Lipids, hydrophobic
40
Transport from ER -> Golgi complex -> Plasma membrane is called
exocytosis
41
Exocytosis can result in 3 protein locations
1)Transmembrane proteins in cell membrane 2) Peripheral membrane association with outer leaflet of cell membrane 3)Release of proteins to extra cellular space
42
Biological membranes exist between the
Solid and fluid state
43
Fluidity of membranes must be
Regulated for normal cell function
44
How is fluidity of membranes mediated?
Interactions between fatty acid chains
45
Two characteristics of carry acid chains
Length and saturation
46
What membrane characteristics result in the most fluid membrane?
Unsaturated carry acids (bent), short, loosely packed
47
What membrane characteristics result in the most solid membrane?
Tight packing, saturated fatty acids, long
48
What other molecule can be found in the membrane that alters fluidity?
Membrane fluidity is also regulated by the presence of cholesterol -cholesterol is also amphipathic (like phospholipids)
49
What interactions in the phospholipid bilayer are disrupted by applying heat?
More heat energy is transferred to phospholipids, which increases their KE, and causes them to denature
50
How do the interactions differ compared to those found in DNA denaturation?
DNA denaturation includes the breaking of H bonds, which changes the overall DNA molecule. The phospholipids bilayer interactions involve Chang’s in fluidity, permeability, and stability.
51
Describe the quaternary structure of clathrin
A major coat protein, required to deform the membrane into a vesicle. -Triskelion (all protein subunits together) -Contains 3 light chains (protein subunits) and 3 heavy chains (protein subunits)
52
COP II goes to
ER to golgi
53
COP I goes to
Golgi to ER
54
Describe the path of clathrin
Clathrin, Golgi, endosome, cell membrane
55
What is one outcome if clathrin failed to function?
Clathrin coat would not protect the vehicle and the vehicle will not be formed. Vesicle cannot form at all
56
What is the role of dynamin in vesicle budding?
Dynamin gets tighter and tighter until the vesicle pops off. Dynamin is a GTPase protein that use GTP hydro;uses for final vesicle budding
57
What is one outcome if dynamin failed to function?
The vesicle will form, but will be stuck on the membrane
58
What is the general pattern of cytoskeletal elements in a cell?
actin and micro tubules (more often moving on actin) -actin is close to PM after transport via cytoskeleton, SNARE proteins facilitate fusion to target membranes
59
How do Tsnares and Vsnares differ in location?
Vsnares - vesicle Tsnares - target Together make the SNARE complex
60
In which step is vesicle transport in the G-protein Rab active
Vesicle transport (Rab GTP is required for vesicle transport)
61
Function of RIP
Ribosome inactivating protein
62
Function of lectin
Sugar binding protein
63
Function of A-chain vs B-chain of lectin
A chain (ricin glycosydase) removes a purine from RNA. B-chain binds to carbs on a cells surface. The toxic A chains are very efficient and one molecule inactivates a few thousand ribosomes per minute
64
In which cellular space is CFTR translation completed
Endoplasmic reticulum because ribosomes perform translation of proteins on the rough ER
65
The transmembrane domains (TMD1 and 2) consist of ____ amino acids
Charged. Composed of hydrophobic, no polar amino acids. The other regions outside the cell are charged and polar amino acids
66
The intracellular and extra cellular loops consist of _____ amino acids
Polar, these regions are exposed to the aqueous environment, which contain polar amino acids. The loops can then interact with water and other molecules
67
What is the major molecular function of the CFTR regarding symptoms of CF?
Facilitate movement of chloride ions across the cell membrane (lack of regulation)
68
What are the two main mechanisms of degradation in the cell?
Remove unfolded protein (requires proteasome), removes damaged organelles (damaged MT can leak ROS, requires process of autophagy)
69
What might be the result if misfolded proteins are not degraded?
Some nonfunctional proteins can be harmful because they gain harmful mutations or accumulate aggregates -protein aggregation in cells can lead to disease -damaged mt produce dangerous byproducts
70
3 steps of fixing protein misfolding
1) Gylycosylation 2) Chaperone proteins 3)Disulfide proteins
71
Glycosylation
Addition of sugars Glucosyltransferase
72
Chaperone proteins
Proteins (BiP/calnexin) Facilitate protein folding
73
Disulfide bonds
Covalent bonds between cysteine amino acids Protein disulfide isomers (PDI) can break and reform bonds
74
What might be the reason for one or two misfolded proteins?
Small, non-recurring problems
75
What might be the reason for a massive buildup of misfolded proteins?
Large scale recurring proteins produce many misfolded proteins
76
What is a first thing a cell will try when misfolded proteins are detected?
Protein refolding, ERAD, UPR
77
ERAD
Endoplasmic reticulum associated degradation Export to proteasome
78
UPR
Unfolded protein resoponse Signals a global response to reduce protein production, fix misfolded protein, or even cell death
79
Problem: Free cysteines (lack of disfulfide bonds)
Fix: PDI tries to reform bonds
80
Problem 2: Improper glycosylation
Fix 2: Glucosyltransferase tries to reglycosylate
81
3a: Problem: Exposed hydrophobic domains
Fix 3: Chaperones like BiP try to help refold protein
82
Steps of ERAD
1) Identification of terminally misfolded proteins 2) export via sec61 3)Ubiquination of the misfolded proteins 4)Degradation by the proteasome
83
What characteristics would indicate that a protein should enter the ERAD pathway?
Defolded/misfolded protein
84
A misfolded protein needs to move from ______ to ___ in order to be degraded by the proteasome
ER, cytoplasm
85
What type of macromolecule is ubiquitin
Protein Misfolded proteins are ubiquinated in the cytoplasm
86
Which type of macromolecule does the proteasome degrade?
Other proteins
87
Which type of organelle is the proteasome?
Nonlysosomal protease complex in the cell Contains catalytic site for degradation of proteins Composed of one 20S core protease subunit and two 19S regulatory subunits to make a 26S holoenzyme
88
What type of bond does the proteasome break?
Peptide bonds between amino acids
89
Why is it important for the 19S subunit to unfold the protein?
19s subunit controls entry and unfolding -unfolding requires atp -bonds and removes ubiquitin
90
20S core subunit is
Structural and catalytic -alpha subunits are structural -beta subunits have protease activity, break peptide bonds
91
Which subunit is required for protease activity
20S
92
Does the proteasome exhibit quaternary structure?
Yes, b/c there are alpha and beta subunits
93
If glycosylation activity is reduced what will not be added to the mature protein
Sugars
94
Why is there a bi-directional arrow between folded and misfolded protein
Changes ER environment and causes a shift from improper and protein folding
95
Two functions of BiP
UPR= ER membrane protein activates transcription factors BiP binds ER integral membrane protein normally -misfolded proteins attract BiP to exposed hydrophobic regions, inhibition of ER membrane proteins is released and UPR is initiated
96
What type of problem might result in UPR activation
DNA mutation
97
3 outcomes of UPR
1)Increase gene expression of proteins that help with refolding processed in ER (PDI or chaperones) 2)Increase gene expression of proteins that help with ERAD (proteasome) 3)Decrease unnecessary protein translation (prevents the buildup of misfolded proteins)
98
What is the common goal of the three outcomes of UPR?
UPR activates transcription factor to increase specific gene expression
99
Autophagy
Degrades misfolded protein clumps in cytoplasm and damaged organelles in cytoplasm using a lysosome
100
Which degradative process would recycle misfolded CFTR protein?
Lysosomal (protein clumps too large for proteasome)
101
Which degradative process would recycle damaged mitochondria?
Proteasome-mediated
102
In autophagy, membrane function
Membranes form around damaged cellular contents to form autophagosome
103
What happens after the autophagosome forms?
Fuses with lysosome resulting in breakdown of contents

PSU Freshman (12 decks)

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