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Flashcards in 8.29.16 Lecture Deck (73):
1

The cytosol of a mammalian cell is divided by ___ into specialized compartments.

Membranes

2

Describe the basic composition of a mammalian cell vis a vis cytosol and organelles.

50% cytosol, 50% organelles

3

The majority of a cell's membrane is found ___.

Internally

4

What are the organelles typically found in a cell?

Nucleus, endoplasmic reticulum, mitochondrion, Golgi apparatus, peroxisome, lysosome, endosome, free polyribosomes

5

Approximately how many mitochondrion are found in the cell?

~200

6

The nucleus is ~___ of cell volume and its membrane is continuous with the ___.

10%; ER

7

What organelles are involved in the sorting and exocytic networks?

ER, Golgi, secretory vesicles

8

What organelles are involved in the endocytic network?

Plasma membrane, endosomes, lysosomes

9

___ are derived from the ER.

Peroxisomes

10

Internal luminal compartments are ___ to the outside of the cell.

Topologically equivalent

11

Translation occurs in the ___.

Cytosol

12

Gated transport takes place ___ between the cytosol and the ___.

Bidirectionally; nucleus

13

Transmembrane transport takes place ___ between the cytosol and what 4 organelles?

unidirectionally; mitochondria, endoplasmic reticulum, plastids, peroxisomes.

14

Vesicular transport involves what 6 organelles?

Golgi, early endosome, late endosome, lysosome, secretory vesicles, cell exterior

15

Vesicular transport occurs bidirectionally from the Golgi to the ___, ___, and ___.

Late endosome, early endosome, secretory vesicles

16

Vesicular transport occurs unidirectionally from the Golgi to the ___, from the early endosome to the ____, from the late endosome to the ___, and from the secretory vesicles to the ___.

Cell exterior; late endosome; lysosome; cell exterior.

17

What are the three types of transport occurring in the cell?

1. Gated transport
2. Transmembrane transport
3. Vesicular transport

18

What do sorting signals do?

Direct proteins to specific compartments

19

Sorting signals are specified by ___.

the amino acid sequence of the protein

20

What are the two general types of sorting signals?

1. Linear sequences, often at the ends of proteins
2. Several separated regions that form a signal patch when folded

21

What are the general signal peptides for the following actions?
1. Import into the ER
2. Import into the mito
3. Import into the nucleus
4. Import into the peroxisome
5. Export from the nucleus

1. Hydrophobic center
2. Amphipathic alpha helices
3. Basic
4. SKL-COOH
5. Nonpolar

22

The nucleus is bounded by a ___ that is perforated by ~4,000 ___ per cell.

Double membrane; nuclear pores

23

What is the nuclear envelope?

The inner and outer nuclear membranes

24

True or false - nuclear pores are only open sometimes.

False - nuclear pores are always open.

25

The nuclear pore is a complex structure with properties of a molecular ___.

Sieve

26

Nuclear pores contain 8-fiber "___."

Baskets

27

Fibrils of the nuclear pore extend into the ___ and the ___ and adhere to trafficking ___.

Nucleus; cytosol; cargo.

28

The nuclear pore is permeable to molecules ___. Larger cargo requires ___ and ___, and active energy-dependent gated transport.

Less than 60kDa; NES; NLS

29

For larger molecules, transport through the nuclear pore requires participation of what two things?

1. Cargo receptors
2. Ran, a small monomeric GTP binding protein

30

Describe the RAN GTPase cycle.

Ran-GDP moves down its concentration gradient into the cell where RanGEF (guanine nucleotide exchange factor) exchanges GDP for GTP, creating Ran-GTP. Ran-GTP moves down its concentration gradient to the cytoplasm, where RanGAP (GTPase activating protein) dephosphorylates Ran-GTP to Ran-GDP. The cycle can begin again.

31

The concentration of ___ is low in the cytoplasm and high in the nucleus. The concentration of ___ is high in the cytoplasm and low in the nucleus.

Ran-GTP; Ran-GDP

32

Describe the process of nuclear export.

1. A cargo protein with a NES binds an export receptor and Ran-GTP.
2. The complex is exported through nuclear pore fibrils to the cytoplasm.
3. RanGAP converts Ran-GTP to Ran-GDP. This breaks the complex and delivers the cargo. Ran-GDP and the export receptor are recycled back to the nucleus.

33

Describe the process of nuclear import.

1. A cargo protein with a NLS binds a receptor protein in the cytoplasm.
2. The complex moves into the nucleus.
3. Ran-GTP binds to the receptor, which releases the cargo. The cargo is delivered.
4. Ran-GTP-receptor complex moves back to the cytosol where RanGAP dissociates the receptor by dephosphorylating Ran-GTP to Ran-GDP.

34

True or false - nuclear export and import signals can be reused during repeated rounds of mitosis.

True

35

Why can nuclear import and export signals be reused during repeated rounds of mitosis?

The nucleus breaks down during each cycle, releasing its proteins. The NLS are still found on the proteins so that after mitosis, they can return to the correct locations.

36

Gene transcription can be regulated by controlling access of ___ to the nucleus. Give an example of this.

Transcription factors; The nuclear uptake of NF-kappaB regulated by phosphorylation of I-kappaB

37

Describe the regulation of NF-kappaB.

NF-kappaB is bound to I-kappaB, which keeps NF-kappaB in the cytosol. Phosphorylation of I-kappaB unbinds I-kappaB and targets it for degradation by the proteasome. NF-kappaB can then enter the nucleus and activate transcription to help regulate cell growth and survival.

38

The mitochondrion is bounded by two membranes, creating four compartments. What are they?

1. Outer membrane
2. Intermembrane space
3. Inner membrane
4. Matrix space

39

Describe the origins of mitochondria.

The mitochondrion was probably a prokaryotic endosymbiont. The inner membrane was the membrane of the endosymbiont. the outer membrane was the endosomal membrane of that which engulfed the symbiont.

40

Despite the fact that the mitochondria have their own DNA genome and make many of their own proteins...

...many proteins of the mitochondria are encoded by the nuclear genome and thus must be transported to the mitochondria.

41

Protein import into the mitochondrial matrix requires ___ and ___ complexes.

TOM (translocase of outermembrane); TIM (translocase of inner membrane)

42

Protein important into the mitochondrial matrix is ___, though the protein is not fully folded at this point.

Post-translational

43

Describe the process of protein import into the mitochondria.

1. Recognition: the signal sequence of the precursor protein is recognized by TOM and binds to TOM receptors.
2. Insertion into the membrane by TOM occurs; the protein is also fed through the TIM complex.
3. Translocation into matrix
4. Cleavage by signal peptidase (the signal is no longer necessary)

44

Protein import into the mitochondrial matrix requires what three things? Explain.

1. Electrochemical gradient: the potential across the inner membrane is dissipated to "electrophorese" the unfolded protein into the matrix.
2. Heat shock proteins (Hsp70): Bind the unfolded cargo protein, push the protein through the pore on ATP hydrolysis-dependent release.
3. Mitochondrial chaperones bind to the unfolded cargo protein and pull the protein through the pore on ATP hydrolysis-dependent release.

45

What are two general types of mitochondrial chaperones? What do they have in common?

Hsp70 and GroEL/GroES - both are ATP-dependent

46

___ disease is associated with mutations in a protein that impedes mitochondrial protein import by binding TIM23.

Huntington's

47

What are the major functions of the peroxisome?

1. Oxidation of very long chain fatty acids, branched chain fatty acids, cholesterol (to bile acids), some metabolic intermediates and foreign substances
2. Synthesis of plasmalogens (membrane lipids found in myelin)
3. Decomposition of hydrogen peroxide

48

Peroxisome precursor vesicles arise by budding of the ___ membrane.

ER

49

Peroxisome precursor vesicles likely expand by ___ and by uptake of specific peroxisomal ___ and ___.

Fission; proteins; lipids

50

Peroxisomal proteins are imported from the ___ after their synthesis is completed.

Cytosol

51

What are the two general signal peptides for peroxisomal proteins?

1. PTS1 (at C-term)
2. PTS2 (at N-term)

52

Transmembrane transport between the cytosol and the ER occurs ___.

Co-translationally

53

___% of cell volume is made up of the ER.

10

54

___% of protein synthesis occurs on the rough ER.

50

55

What are the functions of the ER?

1. Site of membrane/secreted protein creation
2. Site of lipid biogenesis
3. Calcium storage (in smooth ER)
4. Detox of lipid-soluble drugs and poisons

56

What are the three types of ER?

Smooth, rough, and transitional

57

What happens at the transitional ER?

Where vesicles with ER cargo are budded off

58

A common pool of ribosomes is used for what two processes?

1. Synthesis of proteins that stay in the cytosol
2. Synthesis of proteins that are transported to the ER

59

___ binds to the signal peptide that indicates transport to the ER. This then binds to the receptor on the ER membrane.

SRP

60

During the membrane bound ribosome cycle, translation continues when...

...the ribosome is positioned above the transmembrane pore Sec61.

61

A small subset of proteins are inserted ___ into ER membranes.

Post-translationally

62

Membrane proteins contain ___-transfer and ___-transfer signals. These are the charged residues that flank a ___ stretch of protein.

Stop; start; hydrophobic

63

When the amino-terminus is on the lumenal side (in the ER) and the carboxy-terminus is in the cytosol, this is termed ___ and ___.

N-ecto, C-endo

64

When the carboxy-terminus is on the lumenal side (in the ER) and the amino-terminus is in the cytosol, this is termed ___ and ___.

C-ecto, N-endo

65

___ can indicate the number of passes a transmembrane protein makes through the membrane.

Hydropathy plots

66

Proteins in the lumen of the ER are ___ on Asn residues in the following sequence: ___.

Glycosylated; Asn-X-Ser/Thr

67

What are the two types of glycosylation?

1. N-linked (occurs on Asn)
2. O-linked (occurs on Ser or Thr)

68

What are the 5 functions of N-linked glycosylation?

1. Control protein folding
2. Protect underlying protein from proteases, antibodies, and other attacks
3. Add hydrodynamic volume to the protein
4. Operate a part of a sorting signal
5. Provide intercellular communcation

69

What is the main function of O-linked glycoslyation?

1. Absorb water and create a mucus to line lungs and intestinal epithelia, protecting the cell.

70

Proteins failing to fold properly are ___ to the cytosol and degraded by ___.

Retrotranslocated; proteasomes

71

Buildup of unfolded proteins triggers ___.

UPR (unfolded protein response)

72

What is the process of UPR?

1. Misfolded proteins in the ER signal the need for more chaperones by activating a transmembrane kinase.
2. The activated kinase dimerizes and forms an endoribonuclease.
3. The endoribonuclease cuts specific RNA molecules at two positions, removing an intron.
4. 2 exons are ligated to form an active mRNA.
5. The mRNA is translated into a gene regulatory protein.
6. The gene regulatory protein enters the nucleus, activates genes encoding ER chaperones.
7. Chaperones are made in the ER where they help fold proteins.

73

Describe the feedback mechanism from ER/Golgi to nucleus and back to ER to control cholesterol levels.

When cholesterol is high, it binds SCAP and holds SREBP in the ER. When cholesterol is low, SCAP and SREBP are transported to the Golgi. A protease cuts SREBP. The released fragment goes to the nucleus to activate cholesterol biosynthesis genes.