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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
Q

Describe the covalent bond that is formed and the bond that is broken by the peptidyl transferase center of the ribosome?

A

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

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26
Q

Compare and contrast the ribozyme with the other non-coding RNA’s

A

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

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27
Q

How many nucleotides does the ribosome move during translocation?

A

3 nucleotides along the mRNA molecule

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28
Q

What is the name of the G-protein that function in this event?

A

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

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29
Q

Termination occurs

A

when a stop codon is encountered

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30
Q

Termination has a release factor that binds to

A

codon in A site, which triggers hydrolysis of GTP, new peptide chain released.
After hydrolysis, the ribosome complex dissociates

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31
Q

Hierarchy of protein structure

A

Primary
-AA structure
Secondary
-H bonds of backbone
Tertiary
-Interactions between R groups
Quaternary
-Multiple subunits

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32
Q

Secondary structure has

A

alpha helices and beta sheets and is stabilized by backbone

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33
Q

Super secondary structure occurs when

A

2-4 secondary structures interact

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34
Q

Tertiary structure is mediated by

A

H-bonds, disulfide bonds (covalent) and/or hydrophobic reactions

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35
Q

A protein domain is a part of protein that can

A

evolve, function and exist independent of the rest of the protein

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36
Q

Domains dictate the

A

functionality of the protein

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37
Q

A structural motif is a functional part of a protein defines by

A

super secondary structure
-cannot function without the rest of the protein

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38
Q

What are the 3 main destinations of translated proteins?

A

Cytoplasm, endosymbiotic organelles or nucleus(transport of proteins after translation0, and endomembrane system

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39
Q

What macromolecule can be post-translationally added to a protein, so it localizes to the inner (or outer leaflet) of the cell membrane? Why?

A

Lipids, hydrophobic

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40
Q

Transport from ER -> Golgi complex -> Plasma membrane is called

A

exocytosis

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41
Q

Exocytosis can result in 3 protein locations

A

1)Transmembrane proteins in cell membrane
2) Peripheral membrane association with outer leaflet of cell membrane
3)Release of proteins to extra cellular space

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42
Q

Biological membranes exist between the

A

Solid and fluid state

43
Q

Fluidity of membranes must be

A

Regulated for normal cell function

44
Q

How is fluidity of membranes mediated?

A

Interactions between fatty acid chains

45
Q

Two characteristics of carry acid chains

A

Length and saturation

46
Q

What membrane characteristics result in the most fluid membrane?

A

Unsaturated carry acids (bent), short, loosely packed

47
Q

What membrane characteristics result in the most solid membrane?

A

Tight packing, saturated fatty acids, long

48
Q

What other molecule can be found in the membrane that alters fluidity?

A

Membrane fluidity is also regulated by the presence of cholesterol
-cholesterol is also amphipathic (like phospholipids)

49
Q

What interactions in the phospholipid bilayer are disrupted by applying heat?

A

More heat energy is transferred to phospholipids, which increases their KE, and causes them to denature

50
Q

How do the interactions differ compared to those found in DNA denaturation?

A

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
Q

Describe the quaternary structure of clathrin

A

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
Q

COP II goes to

A

ER to golgi

53
Q

COP I goes to

A

Golgi to ER

54
Q

Describe the path of clathrin

A

Clathrin, Golgi, endosome, cell membrane

55
Q

What is one outcome if clathrin failed to function?

A

Clathrin coat would not protect the vehicle and the vehicle will not be formed. Vesicle cannot form at all

56
Q

What is the role of dynamin in vesicle budding?

A

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
Q

What is one outcome if dynamin failed to function?

A

The vesicle will form, but will be stuck on the membrane

58
Q

What is the general pattern of cytoskeletal elements in a cell?

A

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
Q

How do Tsnares and Vsnares differ in location?

A

Vsnares - vesicle
Tsnares - target
Together make the SNARE complex

60
Q

In which step is vesicle transport in the G-protein Rab active

A

Vesicle transport
(Rab GTP is required for vesicle transport)

61
Q

Function of RIP

A

Ribosome inactivating protein

62
Q

Function of lectin

A

Sugar binding protein

63
Q

Function of A-chain vs B-chain of lectin

A

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
Q

In which cellular space is CFTR translation completed

A

Endoplasmic reticulum because ribosomes perform translation of proteins on the rough ER

65
Q

The transmembrane domains (TMD1 and 2) consist of ____ amino acids

A

Charged. Composed of hydrophobic, no polar amino acids. The other regions outside the cell are charged and polar amino acids

66
Q

The intracellular and extra cellular loops consist of _____ amino acids

A

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
Q

What is the major molecular function of the CFTR regarding symptoms of CF?

A

Facilitate movement of chloride ions across the cell membrane (lack of regulation)

68
Q

What are the two main mechanisms of degradation in the cell?

A

Remove unfolded protein (requires proteasome), removes damaged organelles (damaged MT can leak ROS, requires process of autophagy)

69
Q

What might be the result if misfolded proteins are not degraded?

A

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
Q

3 steps of fixing protein misfolding

A

1) Gylycosylation
2) Chaperone proteins
3)Disulfide proteins

71
Q

Glycosylation

A

Addition of sugars
Glucosyltransferase

72
Q

Chaperone proteins

A

Proteins (BiP/calnexin)
Facilitate protein folding

73
Q

Disulfide bonds

A

Covalent bonds between cysteine amino acids
Protein disulfide isomers (PDI) can break and reform bonds

74
Q

What might be the reason for one or two misfolded proteins?

A

Small, non-recurring problems

75
Q

What might be the reason for a massive buildup of misfolded proteins?

A

Large scale recurring proteins produce many misfolded proteins

76
Q

What is a first thing a cell will try when misfolded proteins are detected?

A

Protein refolding,
ERAD,
UPR

77
Q

ERAD

A

Endoplasmic reticulum associated degradation
Export to proteasome

78
Q

UPR

A

Unfolded protein resoponse
Signals a global response to reduce protein production, fix misfolded protein, or even cell death

79
Q

Problem: Free cysteines (lack of disfulfide bonds)

A

Fix: PDI tries to reform bonds

80
Q

Problem 2: Improper glycosylation

A

Fix 2: Glucosyltransferase tries to reglycosylate

81
Q

3a: Problem: Exposed hydrophobic domains

A

Fix 3: Chaperones like BiP try to help refold protein

82
Q

Steps of ERAD

A

1) Identification of terminally misfolded proteins
2) export via sec61
3)Ubiquination of the misfolded proteins
4)Degradation by the proteasome

83
Q

What characteristics would indicate that a protein should enter the ERAD pathway?

A

Defolded/misfolded protein

84
Q

A misfolded protein needs to move from ______ to ___ in order to be degraded by the proteasome

A

ER, cytoplasm

85
Q

What type of macromolecule is ubiquitin

A

Protein
Misfolded proteins are ubiquinated in the cytoplasm

86
Q

Which type of macromolecule does the proteasome degrade?

A

Other proteins

87
Q

Which type of organelle is the proteasome?

A

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
Q

What type of bond does the proteasome break?

A

Peptide bonds between amino acids

89
Q

Why is it important for the 19S subunit to unfold the protein?

A

19s subunit controls entry and unfolding
-unfolding requires atp
-bonds and removes ubiquitin

90
Q

20S core subunit is

A

Structural and catalytic
-alpha subunits are structural
-beta subunits have protease activity, break peptide bonds

91
Q

Which subunit is required for protease activity

A

20S

92
Q

Does the proteasome exhibit quaternary structure?

A

Yes, b/c there are alpha and beta subunits

93
Q

If glycosylation activity is reduced what will not be added to the mature protein

A

Sugars

94
Q

Why is there a bi-directional arrow between folded and misfolded protein

A

Changes ER environment and causes a shift from improper and protein folding

95
Q

Two functions of BiP

A

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
Q

What type of problem might result in UPR activation

A

DNA mutation

97
Q

3 outcomes of UPR

A

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
Q

What is the common goal of the three outcomes of UPR?

A

UPR activates transcription factor to increase specific gene expression

99
Q

Autophagy

A

Degrades misfolded protein clumps in cytoplasm and damaged organelles in cytoplasm using a lysosome

100
Q

Which degradative process would recycle misfolded CFTR protein?

A

Lysosomal (protein clumps too large for proteasome)

101
Q

Which degradative process would recycle damaged mitochondria?

A

Proteasome-mediated

102
Q

In autophagy, membrane function

A

Membranes form around damaged cellular contents to form autophagosome

103
Q

What happens after the autophagosome forms?

A

Fuses with lysosome resulting in breakdown of contents

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