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BIOL 200 > Unit 4 > Flashcards

Unit 4 Flashcards

1
Q

Where does translation begin? Is there an order to how subunits are attached?

A

the cytosol. Random order - any large subunits can attach to any small subunits - mix and match

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2
Q

Polyribosomes

A

Multiple ribosomes work simultaneously on a single mRNA. As soon as a ribosome has translated enough of the nucleotide sequence to move out of the way, a new ribosome binds to the 5’ end of the mRNA

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3
Q

When are proteins folded?

A

During translation

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4
Q

The endomembrane system

A

Membrane compartments involved in synthesis/processing and movement of proteins, lipids, and carbohydrates

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5
Q

Requirements for protein import into an organelle

A

1) A specific signal sequence in the protein primary sequence
2) A specific protein receptor on the organelle of interest

NOTE: proteins do not have to be fully translated or fully folded

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6
Q

Where do proteins enter the endomembrane system?

A

They enter the ER and they never return to the cytosol. They either stay in the ER or continue to move to other organelles of the endomembrane system

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7
Q

Are rER and sER separate and discrete membranes?

A

No - they are continuous and interconnected. Lumen and membrane of rER and sER are connected because they are one organelle. The sER and rER ratio depends for every cell

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8
Q

Import to the ER signal sequence

A

Consists of many nonpolar amino acids. 20-27 AAs at the N-terminus serve as the signal sequence (start transfer sequence). It contains a segment of approx. 10< hydrophobic AAs

Determines location and orientation in the ER

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9
Q

When is the signal for entry into the ER recognized?

A

Before translation of the protein is complete

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10
Q

What are the differences between ER membrane-bound and free ribosomes?

A

1) they differ only in the proteins they are making at a particular time
2) they differ in their sequence, if they contain a signal sequence that targets them to the ER or not

Otherwise, they are structurally and functionally identical

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11
Q

Post-translational trafficking of proteins

A

Ribosomes remain “free” in the cytosol

Completed polypeptide goes to its functional destination depending on its sorting signal

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12
Q

Co-translational trafficking of protiens (protein is not fully finished)

A

Ribosomes attach to ER membrane

Protein is threaded through ER membrane as it’s being translated

Proteins either stay in the ER, or continue to other compartments of the endomembrane system

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13
Q

Name 4 examples of proteins that would you expect to be targeted to the ER

A

1) Soluble proteins destined for secretion
2) Lysosome resident proteins
3) Enzymes required for protein glycosylation
4) Plasma membrane transmembrane proteins

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14
Q

How does a protein stay in the lumen of the ER?

A

The protein should have a retention signal, called the KDEL sequence

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15
Q

Targeting sequence in the primary sequence function

A

Directs the protein to a specific organelle

Must be present for protein to leave the cytosol compartment

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16
Q

2 targeting requirements to the ER

A

1) Signal sequence encoded within the protein

2) Receptor that recognizes and binds the signal (SRP - signal recognition particle)

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17
Q

Signal recognition particle (SRP) as the ER receptor

A

SRP recognizes the ER signal sequence (start transfer seq) and directs the protein to the ER

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18
Q

Co-translational transport across the ER membrane steps

A

1) SRP binds to the exposed ER signal seq and to the ribosome (and slows down protein synthesis)
2) SRP-ribosome complex binds to SRP receptor in the ER membrane. SRP is released and ribosome is passed on to the protein translocation channel
3) ER signal seq binds the protein translocation channel and opens it, and polypeptide chain gets threaded through the channel across the lipid bilayer

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19
Q

What does the primary seq of the proteins determine according to the ER

A

Location in the ER and orientation in the ER membrane

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20
Q

Start transfer seq (N-terminal signal seq or N-terminal start transfer seq) and internal start transfer seq

A

Initiates transfer of protein across membrane. It is cleaved off

Initiates transfer of protein across membrane. It is a membrane-crossing domain and not cleaved off

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21
Q

Stop transfer seq

A

Stops transfer of protein across membrane. It is a membrane-crossing domain

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22
Q

Where will a protein with only an N-terminal ER signal seq ultimately end up?

A

Outside the cell - once it is in the ER, it cannot go back to the cytosol. Since it has a signal seq, it will go to the ER but will not stay since it does not have a retention signal

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23
Q

Where will a protein with an N-terminal ER signal seq and an NLS ultimately end up?

A

Outside the cell - the NLS might not be translated. The protein needs to be fully made before it goes to the nucleus. ER doesn’t need a fully-formed protein

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24
Q

Orientation of transfer sequences

A

First transfer seq is the “start” transfer seq and allows the polypeptide to feed into the ER after the seq. If it is at the N-terminus, it will be cleaved off after protein synthesis

Stop transfer seq follows start. causes polypeptide to stop entering the ER after stop seq

Stop and start seq alternate when several are present

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25
Q

Function of ER regarding protein processing

A

Protein folding
Covalent modification
Disulfide bond formation
Glycosylation

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26
Q

Protein folding in the ER

A

Proteins fold via hydrophobic interactions. When there are many polypeptides being synthesized and co-translated, they can form unwanted interactions with each other, which can result in new polypeptides clumping. In the ER, chaperone proteins prevent this by “holding on” to the proteins until they fold properly. They also prevent misfolded proteins/partially assembled proteins from leaving the ER

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27
Q

Chaperone proteins production in the ER

A

Misfolded proteins in the ER lumen initiate the production of chaperone proteins. Feedback loop.

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28
Q

What happens to misfolded proteins?

A

They are tagged with ubiquitin and sent back to the cytosol and degraded by to proteasome. AAs are recycled

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29
Q

After the translation on ribosomes in the cytosolic compartment, where are proteins processed?

A

Either in the cytosol or in the ER/Golgi system

30
Q

Glycosylation - oligosaccharide units

A

Begins in the ER. An oligosaccharide “tree” is added to dolichol (a phospholipid) on the cytosolic face of the ER membrane. Then a flippase enzyme flips dolichol in the membrane so the oligosaccharide tree is in the ER lumen side. Lastly, the tree is transferred from dolichol to the growing polypeptide chain, where a transferase enzyme recognizes the Asn-X seq and links the tree to it. Glycoprotein is packaged into vesicle and sent to Golgi. Based on the protein structure, sugars are added, and this overall structure determines where it is sent

31
Q

What happens to the oligosaccharide in the Golgi

A

In the Golgi and the ER, the oligosaccharide is trimmed, then in the Golgi, new sugars are added to the oligosaccharide one at a time

32
Q

Requirements for vesicles to take the correct cargo from the donor compartment to the correct target compartment

A

Cargo getting into the correct vesicle depends on the vesicle protein coats. The vesicle getting to the correct destination depends on Rab proteins, Tethers, and Snares

33
Q

Vesicle formation

A

The cargo protein is recognized by the cargo receptor and bind in the membrane. The adaptor proteins recognize and bind to the cytosolic portion of the receptor and the coat proteins bind to the adaptor proteins. These coat proteins bend the membrane into vesicles and the vesicle pinches off from the donor membrane

34
Q

Steps of a vesicle budding off

A

The process is regulated by GTP-binding protein. When it is bound the GTP, it is active and allows adaptors and coat proteins to bind. When GTP is hydrolyzed to GDP, it becomes inactive and GTPases (binds GTP and helps assemble membrane coat), coat proteins, and adaptors dissociate from vesicle

35
Q

What would happen if the dynamin protein is defective?

A

The dynamin protein acts as a pair of molecular scissors and helps newly formed vesicle proteins to bud off from the plasma membrane. If it is defective, the vesicles cannot bud off

36
Q

Do all newly forming vesicles require adaptin, clathrin, and dynamin on the cytosolic face of the membrane?

A

No, there are different adaptors and coat proteins involved in vesicle formation in the cytosol, such as clathrin, COPI, and COPII

37
Q

Clathrin-coated vesicles

A

Involved in PM to endosome traffic (endocytosis) and Golgi to lysosome (via endosome). Dynamin is required for budding

38
Q

COPI-coated vesicles

A

Involved in Golgi to ER traffic (retrieval). Dynamin not requried

39
Q

COPII-coated vesicles

A

Involved in ER to Golgi traffic (forward). Dynamin not required

40
Q

Two proteins that direct vesicles to the right place for docking

A

1) Rabs are proteins that are lipid-linked to the membrane

2) Tethers are proteins that bind to the Rab on the vesicle and pull them into the PM, which eventually fuse

41
Q

2 proteins that mediate vesicle fusion

A

1) v-SNAREs are on vesicle membranes and are made up of one protein
2) t-SNAREs are on the target membrane and are made up of two or more proteins

42
Q

Difference between Golgi in mammalian and plant cells

A

In mammalian cells, the Golgi is a singular perinuclear stack, while plant cells have small stacks on tracks that move around the cell (b/c of cytoskeleton)

43
Q

Cisternae of Golgi

A

Each one contains different enzymes that modify the proteins that pass through it, via adding/removing sugars to the oligosaccharide (covalent bonds)

44
Q

Protein sorting in Golgi

A

Proteins in the cis face can either move forward, stay in cis Golgi, or return to the ER via retention signal

Proteins in the trans face are sorted via their oligosaccharide signal as regulated secretion, constitutive secretion, or via the lysosomal pathway

45
Q

2 major proteins in the Golgi

A

Cargo proteins - passes through Golgi to move to other destinations in the endomembrane system (ex. proteins to be secreted, sent to lysosome, etc.)

Resident proteins - those that function in the Golgi (ex. glucosyl transferase, etc.)

46
Q

Vesicle transport model

A

Cargo is carried forward from cis to trans in vesicles and resident proteins stay in place in the cisternae (one direction)

47
Q

Cisternal maturation

A

Vesicles carrying the cargo fuse to form the cis-cisternae, where the cargo remains in the cisternae. When a new cis-cisternae forms, the old one “matures” to the medial-cisternae, etc. Resident proteins must move backwards (trans to cis) as cisternae moves forwards (cis to trans)

48
Q

Exocytosis: Constitutive secretion (default secretory pathway)

A

Occurs in all cells and happens continuously. No env signals are needed for vesicle fusion with the PM

It supplies the PM with newly made lipids and proteins, allows it to expand before cell division. Also lets secreted proteins to be incorporated into the cellular matrix, and allows them to nourish or signal other cells

49
Q

Exocytosis: Regulated secretion

A

Only occurs in specialized secretory cells. Proteins are stored in secretory vesicles and are only released when a signal is received (ex. digestive enzymes, insulin, etc.)

It allows the proteins to be secreted rapidly and on demand

50
Q

Lumenal pH

A

As the pH increases, it initiates proteins to form aggregates and they increase in concentration and condense in secretory vesicles. These secretory vesicles lay close to the PM. This occurs to proteins in the secretory pathway

51
Q

Pulse-chase and autoradiography

A

Label one group of molecules via radio active AAs (which is the pulse) and follow where they go over time. Instrumental determination of pathways

52
Q

Green Fluorescent Protein (GFP)

A

Cargo proteins can be tagged with GFP in live cells

53
Q

Mannose-6-phosphate

A

A targeting signal and a phosphorylated sugar that is added onto lysosomal proteins. It is added during the glycosylation in the ER

54
Q

Proteins targeted to lysosomes requirements

A

1) M6P targeting signal

2) M6P receptor

55
Q

Mannose conversion

A

Mannose is phosphorylated to M6P in the cis Golgi

56
Q

Lysosomal pathway

A

M6P signal is added to lysosomal proteins in cis Golgi and the M6P receptor in the membrane of TGN recognizes and binds to the sorting signal. The vesicle is coated in clathrin and sheds it in the cytosol to fuse with an early endosome, with a pH 6 or less env. Lysosomal enzymes dissociate from the M6P receptor in early endosome and phosphatases prevents rebinds with M6P receptor by removing lysosomal enzymes. M6P receptors are recycled back to the trans Golgi

57
Q

Endosomal compartment

A

Acts as a sorting station for proteins arrive from the TNG and cell surface. Early endosome matures into late endosome, which can turn into a lysosome, or fuse with one

58
Q

Lysosome

A

Membrane-enclosed organelle where intracellular degradation occurs. Only works at pH 5. Diverse size and shape

59
Q

Do plants have lysosomes?

A

No, plants don’t have lysosomes, but their vacuoles act as lysosomes

60
Q

Can lysosomes digest their own membrane proteins and lipids?

A

No; they are resistant to their own digestive enzymes because of extensive glycosylation of proteins on the lumen side of the membrane

61
Q

Why don’t lysosomal enzymes (acid hydrolases) digest the cell as soon as they are synthesized and before they reach the lysosome?

A

The enzymes need very low pH (approx. 5) to be activated. This is achieved through ATP hydrolysis to pump protons into lysosomes

62
Q

Endocytosis: Phagocytosis

A

“Cellular eating”. A defense mechanism used to remove unwanted material (ex. bacteria) and target it for degradation in the lysosome. This occurs by pseudopods, which are cell extensions produced by changes in the cell’s cytoskeleton, that engulf the bacteria. No coat proteins are used. The phagosome fuses with lysosomes and the material taken by phagocytosis is degraded by lysosomal enzymes

63
Q

Endocytosis: Pinocytosis

A

“Cellular drinking”. Non-selective process where fluid and macromolecs from extracellular region are taken up freely. No specific receptor required. Carried out by clathrin-coated vesicles. They fuse with an early endosome and the trash goes to late endosome, then lysosome for breakdown. This is a continuous process where cells remove membrane added by exocytosis, allowing recycling of the PM

64
Q

Receptor-mediated endocytosis (RME)

A

Cells internalize parts of the PM, including some fluid and macromolecs in small vesicles from extracellular space. Clathrin is used for vesicle formation

65
Q

Adaptin

A

A bridge between the cargo and the clathrin coat

66
Q

Low Density Lipoprotein (LDL)

A

A large complex that contains lipids and cholesterol as cargo and makes them water soluble. Carries them in blood

67
Q

Compare and contrast receptor recycling in lysosomal and endocytic pathways

A

Early endosomes are sorting centers and recycle M6P receptors back to the TGN in the endocytic pathway. In the lysosomal pathway, the LDL receptors are recycled to the PM

68
Q

Early endosome

A

First to receive all endocytosed material. This is the compartment where receptors are recycled (to the TGN or PM). Can mature to late endosome when amount of material internalized by endocytosis increases

69
Q

Late endosome

A

Don’t recycle material and are purely for degradation, meaning they have a lower pH than early endosomes

70
Q

What happens if there is a mutation in an adaptin that links the LDL receptor to clathrin?

A

There is no link to the receptor, therefore, the vesicle does not form and stays on the plasma membrane. This leads to high cholesterol and heart disease

BIOL 200 (7 decks)

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