Mcb*2050 Final

Front 1

Deconvolution

Back 1

In microscopy: Process of removing background/out-of-focus light to increase contrast and clarity

Front 2

What 2 factors affect resolution in microscopy and how are they altered to maximize resolving power?

Back 2

1) Wavelength of illumination light

2) Numerical aperture (light gathering qualities of objective lens/mounting medium)

- Increasing resolving power = decrease resolution distance. Increase NA or use shorter wavelength of light

Front 3

Which form of microscopy uses wavelength specific lasers, and takes z sections of a specimen that may be living or dead.

Back 3

Confocal Laser Scanning Microscopy

Front 4

What are the components of a transmission electron microscope?

Back 4

- Hollow cylindrical chamber under a vacuum

- Electron gun

- Electromagnetic lenses/magnets

- Viewing screen

Front 5

In microscopy what is the equation for calculating resolution?

Back 5

Resolution (nm) = (0.61 x wavelength)/NA

Front 6

What are the two classes of fluorophores used in microscopy? Give an example of each.

Back 6

Fluorescent proteins (ex. GFP) and small chemical or organic compounds (ex. fluorescein)

Front 7

In relation to chemical fixation of a specimen for microscopy, what are artifacts and why are they observed?

Back 7

Artifacts are observations that are a result of the preparation, not naturally occurring. In this case, all parts of the cell may not be immobilized properly, and result in an altered representation of cell organization and structure.

(Hard to get an accurate "snapshot")

Front 8

What is the form of preparation for electron microscopy in which the specimen is flash frozen using liquid nitrogen and high pressure?

Back 8

Cryofixation

Front 9

What are the steps/stages to preparing a specimen for electron microscopy?

Back 9

1. Fixation

2. Staining (lipids/membranes)

3. Dehydration

4. Embedding (mechanical support)

5. Cutting

6. Post-staining (Heavy-metals to increase e- density of macromolecules in the cell)

Front 10

Place the following from highest to lowest resolving limit (longest to shortest distance between two distinct points)

Electron microscope

Standard brightfield microscope

Super resolution CLSM

CLSM

Human Eye

Back 10

1. Human eye

2. Standard brightfield & CLSM

3. Super resolution CLSM

4. Electron miscrocope

Front 11

How are nuclear lamina attached to the nuclear envelope?

Back 11

Nuclear lamina attach to integral membrane proteins on the inner surface of the inner membrane of the nuclear envelope

Front 12

What is Hutchinson Gilford Progeria syndrome?

Back 12

Mutation in lamin A gene results in destabilization of nuclear lamina leading to premature aging in children and death by adolescence

Front 13

What are the 3 main functions of the nuclear envelope?

Back 13

- Separates genome/cytosol and transcription/translation

- Selective barrier

- Binds nuclear lamina and provides structural framework for nucleus

Front 14

What is the function of interchromosomal channels?

Back 14

Function as barriers between discrete subdomains of the nucleus to prevent unwanted DNA-DNA or DNA-protein interactions

Front 15

What are transcription factories and what is their function?

Back 15

Sections of interchromosomal channels where transcription factors are concentrated. Active chromatin extends out into the section (from its subdomain) to be transcribed

Front 16

What are nuclear speckles and what are their function?

Back 16

Numerous and highly dynamic nuclear subdomains (often beside transcription factories) where mRNA splicing factors are concentrated for processing of pre-mRNA

Front 17

What subdomain of the nucleus is the site for ribosome biogenesis?

Back 17

Nucleolus

Front 18

What component of the nucleus organizes nuclear subdomains and anchors protein factors?

Back 18

Nuclear matrix

Front 19

True or False?

Passage of small molecules through the nuclear pore complex is closely regulated

Back 19

False, small molecules move freely through, large molecules are regulated

Front 20

What is the Classic NLS signal

Back 20

KKQRKK

Front 21

What is the Bipartite NLS signal?

Back 21

KR[spacer]KKKK

Front 22

Is the concentration of Ran-GTP higher in the nucleus or the cytoplasm?

Back 22

Ran-GTP > Ran-GDP in the nucleus

Front 23

What is the role of Rcc1?

Back 23

Rcc1 is a GEF that exchanges GDP for GTP to convert Ran-GDP to Ran-GTP in the nucleus (activating it)

Front 24

What is the role of Ran-GAP1?

Back 24

Ran-GAP1 is a GAP that activates Ran's GTPase activity to release a phosphate from GTP, converting it to Ran-GDP (inactivating it)

Front 25

What are Karyopherins?

Back 25

Transport receptor proteins necessary for the nucleocytoplasmic transport of cargo

Front 26

What are ribonucleoproteins (RNPs)

Back 26

Complex of RNA molecules for nuclear export

Front 27

Where are mutations that affect nucleocytoplasmic transport usually located?

Back 27

In the localization sequence for the cargo protein

Front 28

What are the four general steps of vesicle transport?

Back 28

1. Formation

2. Transportation

3. Fusion

4. Retrotransport

Front 29

What trafficking pathway in the endosomal system transports materials from the ER, and ultimately to the PM or lysosomes?

Back 29

Biosynthetic pathway

Front 30

What trafficking pathway in the endosomal system transports materials from the ER and ultimately to the PM or extracellular space in the form of granules or vesicles?

Back 30

Secretory pathway

Front 31

What is the difference between constitutive and regulated secretion?

Back 31

Constitutive secretion is unregulated, regulated secretion occurs in specialized cells and involves a vesicle that pauses and waits for a cellular signal before releasing its cargo into extracellular space (ex. neurotransmitters)

Front 32

What trafficking pathway in the endosomal system transports materials from the PM to endosomes or lysosomes?

Back 32

Endocytic pathway

Front 33

What mediates the shape and curvature of ER tubules and cisternae?

Back 33

Reticulons (hair-pin structure)

Front 34

What are ERES, MAM, PAM, and the outer nuclear membrane all examples of?

Back 34

Endoplasmic reticulum subdomains

Front 35

What are the four stages of protein processing in the ER?

Back 35

1. Signal sequence cleavage

2. Initial stages of glycosylation

3. Protein folding and assembly

4. Quality control

Front 36

What is the function of glycosylation?

Back 36

To assist the protein in folding, binding to other macromolecule, and targeting within the cell

Front 37

What is N-linked glycosylation?

Back 37

Adding sugar monomers to the terminal amino group of the asparagine residues of a protein

Front 38

Which residues will receive N-linked glycosylation?

Back 38

Lumenal facing asparagine residues that correspond with sequence (N - x - S/T)

Front 39

How does ERAD relate to cystic fibrosis?

Back 39

Most cystic fibrosis patients have a mutant transporter protein (CFTR) that is degraded by the ERAD pathway instead of being functional and transported to the PM

Front 40

What happens to proteins that continue to misfold in the ER?

Back 40

Slow-acting enzyme eats away at mannose residues, eventually identified as a lost cause and transported to the cytosol via translocon where it is poly-ubiquitinated and targeted to the proteasome for degradation

Front 41

Which unfolded protein response pathway involves upregulation of genes associated with mediating proper protein folding?

Back 41

ATF6-mediated pathway

Front 42

Which unfolded protein response pathway involves pausing protein synthesis?

Back 42

PERK-mediated pathway

Front 43

When BiP is bound, does it activate or inactivate PERK and ATF6?

Back 43

Inactivates, when it is released to help with folding it activates them.

Front 44

Where are ERES located?

Back 44

Part of the endoplasmic reticulum located close to the cis Golgi portion of the Golgi

Front 45

Where do clathrin-coated vesicles form and where is their cargo transported?

Back 45

1) Trans golgi network to late endosome

2) PM (coated pits) as part of receptor-mediated endocytosis to bring receptor-ligand complexes to the early endosome

Front 46

What are the names of the proteins involved in COPII vesicle formation at the ERES?

Back 46

Sar1-GDP/GTP (GEF mediates change), Sec23 and 24, Sec 13 and 31

Front 47

Which COP are involved in anterograde transport?

Back 47

COPII

Front 48

Which COP are involved in retrograde transport?

Back 48

COPI

Front 49

What is the purpose of the multiprotein tethering complex?

Back 49

One of two options for tethering a vesicle to a cell with a molecular bridge, recruited by Rab so that SNAREs can then interact and ultimately the vesicle can fuse with the membrane

Front 50

What is the KDEL sequence and what is its purpose?

Back 50

KKxx = Signal on ER resident proteins as well as KDEL receptors in the Golgi network in order to incorporate escaped proteins into vesicles for retrograde transport back to ER

Front 51

What is the difference between the Golgi in mammalian cells, and the Golgi in plant and yeast cells?

Back 51

In mammals = one large Golgi complex

In plants/yeast = numerous Golgi complexes throughout

Front 52

What are the two domains of Golgi cisternae and what goes on there?

Back 52

Central domain = site of biochemistry

Irregular domain = site of vesicular transport (periphery)

Front 53

What is the Golgi matrix?

Back 53

Various peripheral and integral membrane proteins (GRASPs) that help hold Golgi subcompartments together and link them to the cytoskeleton (GMAP) and allow communication between ER and cis Golgi

Front 54

Which parts of the Golgi are considered protein sorting stations?

Back 54

cis Golgi network and trans Golgi network

Front 55

If a protein's core oligosaccharide has galactose, fucose, and sialic acid residues added as the final glycosylation step in the trans golgi network, what is its destination?

Back 55

Plasma membrane

Front 56

How are proteins destined for the lysosome recognized in the cis Golgi network?

Back 56

Signal patch

Front 57

How are proteins destined for the lysosome recognized in the trans Golgi network?

Back 57

Mannose-6-phosphate groups that were added in cis and medial

Front 58

What is the difference between N-linked glycosylation and O-linked glycosylation?

Back 58

N-linked glycosylation begins in the ER and is completed in the Golgi, O-linked glycosylation occurs entirely in the Golgi

Front 59

What is the most accepted model for movement of material through the Golgi complex?

Back 59

Cisternal progression/maturation model, where Golgi subcompartments are dynamic, CGN forms from COPii-vesicles that left ER, then changes and progresses from cis to trans, with COPI vesicles moving resident Golgi proteins backwards to keep them in their proper subcompartment

Front 60

What is the structure in a plant or yeast cell that is equivalent to a lysosome?

Back 60

Vacuole

Front 61

What proteins are involved in the formation of clathrin-coated vesicles in the TGN?

Back 61

Arf1-GDP/GTP, GGA, M6P receptors, clathrin, dynamin

Front 62

What does clathrin consist of?

Back 62

Three light chain polypeptides and three heavy chain polypeptides that form a triskelion

Front 63

What is a clathrin lattice?

Back 63

A 3D pentagonal structure formed by clathrin triskelions that mediates membrane curvature in a forming vesicle

Front 64

Order the following in terms of increasing acidity (decreasing pH): lysosome, early endosome, cytosol, late endosome

Back 64

1. Cytosol

2. Early endosome

3. Late endosome

4. Lysosome

Front 65

What proteins/lipids are involved in the formation of clathrin-coated vesicles from the PM?

Back 65

Receptor-ligand complexes, PIP2, AP2, clathrin, dynamin

Front 66

What proteins/lipids are involved in the fusion of mitochondria?

Back 66

OM = Mfn1 and Mfn2 (regulated by Bax), cardiolipin/phosphatidic acid (phospholipase D), IM = OPA1 (regulated by prohibitin)

Front 67

What proteins/lipids are involved in the fission of mitochondria?

Back 67

Fis1, MiD, Mff, Drp1(GTP bound)

Front 68

What is responsible for targeting a protein to the mitochondria and the subsequent subcompartment?

Back 68

Presequence (amphipathic, alpha helix, dual purpose)

Front 69

What are the proteins/complexes involved in targeting and import of a protein to the mitochondrial matrix? What are their roles?

Back 69

Hsp70 = keeps protein partially unfolded

TOM = recognizes presequence

TIM23 = Protein passed off to/goes through as trying to escape the +ly charged IMS

mtHsp70 = motor/ratchet to pull protein into matrix/prevent backsliding, + helps fold

MPP (matrix protease) = cleaves presequence

Front 70

Order the following in terms of progression of autophagy of a damaged organelle: autolysosome, residual body, phagophore, autophagosome, damaged organelle

Back 70

1. Damaged organelle

2. Phagophore

3. Autophagosome

4. Autolysosome

5. Residual body

Front 71

What are the two possible fates of a residual body in a cell?

Back 71

1. Released into the cytoplasm

2. Retained as a Lipofuscin pigment granule

Front 72

What are the normal roles for PINK1 and Parkin in a healthy cell?

Back 72

PINK1 is synthesized, targeted to the mitochondria, and degraded, and Parkin hangs out in the cytoplasm doing nothing, UNLESS a mitochondria is not functioning properly, then PINK1 accumulates on the OM of mitochondria and recruits Parkin which poly-ubiquitinates OM proteins to signal mitophagy

Front 73

What happens when PINK1 or Parkin is mutated?

Back 73

Damaged mitochondria can't be targeted for mitophagy, and accumulate in the cell, impairing its function and ultimately leading to cell death. (Cells most susceptible to death = dopaminergic neurons)

Front 74

What's the difference between stroma, stroma thylakoids, and stromules?

Back 74

Stroma = aqueous interior of chloroplasts inside of oenvelope and surrounding thylakoids, equivalent to mitochondrial matrix

Stroma thylakoids = thylakoids that connect grana

Stromules = dynamic stroma-filled tubules that connect chloroplasts

Front 75

Where are the genomes of chloroplasts and mitochondria located?

Back 75

Plastid genomes are located in the mitochondrial matrix and in the stroma of chloroplasts

Front 76

What is responsible for targeting most stromal-destined proteins to the chloroplast and then to the stroma?

Back 76

Transit peptide

Front 77

What are the proteins/complexes involved in targeting and import of a protein to the stroma? What are their roles?

Back 77

Hsp70 = keeps protein partially unfolded

TOC (OM) = recognizes transit peptide

TIC (IM) = Protein passed off to pass through IM

Hsp93 = motor/ratchet, pulls through and keeps from backsliding

Stromal processing enzyme = Transit peptide cleavage

Hsp60 = proper folding

Front 78

What differentiates proteins that are destined for the stroma and those destined for the thylakoid lumen?

Back 78

Most thylakoid lumen proteins have a thylakoid transfer domain that is exposed upon removal of transit peptide

Front 79

What are the main functions of peroxisomes?

Back 79

Lipid metabolism and neutralization of free radicals

Front 80

What is a crystalline core?

Back 80

Location of urate oxidase for converting uric acid to allantoin