Cell Structure

Question 1

Cholesterol effect on cell membranes

Answer 1

Stiffens

reduces permeability

inhibits phase changes

Question 2

Membrane Function

Answer 2

*Establishment of specialized environments

*Boundary between inside and outside of cell
*Define intracellular compartments
*Serve as a scaffold to organize protein complexes *(molecular machines) involved in numerous biochemical reactions
*Semi-permeable barrier
*Transport
*Sensing and responding to environment – cell signaling
*Cell protection and identification
*Cell junctions and adhesion

Question 3

What do cystic fibrosis, muscular distrophy and hereditary spherocytosis all have in common?

Answer 3

They are all diseases involving cellular membranes or membrane proteins

Question 4

3 important types include:
Phospholipids
Cholesterol
Glycolipids

Answer 4

*All these lipids are amphipathic – possess hydrophobic and hydrophilic regions
*By mass, phospholipids and sterol make up the bulk of the membrane lipid.
*Phospholipids – 4 major types

*Quantitatively minor - but functionally very important - lipids include glycolipids and a type of phospholipid called phosphatidylinositol
It is estimated that eukaryotic membranes contain 500-1000 distinct types of lipids

Question 5

Glycolipids

Answer 5

Some neutral, some charged
Present only on non-cytosolic leaflet (b/c that’s where enzymes that add sugar part are)
May partition preferentially into lipid rafts
Most complex are gangliosides; negatively charged sialic acid residues; enriched in neurons and apical surfaces of epithelial cells

Functions
Protection (glycocalyx)
Surface properties of membranes
Cell identification
Cell adhesion

Question 6

Phosphotidylinositol

Answer 6

Can be phosphorylated at diff positions by kinases. Diff location –> diff steric surface –> diff fnxn. Diff proteins bind based on where PO4’s are. Phosphatases can de-phosphorylate. Lipases can clip off phosphotols from diacylglycerol parts. Both have diff signaling transduction.

Question 7

How are phosphatydalinositals involved in cell signaling?

Answer 7

1 - binding and activating various enzymes at the membrane surface

2 - serving as a substrate for membrane-associated phospholipases

Question 8

What synthesizes phosphoglycerides (phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine)?

Answer 8

Endoplasmic reticulum

Question 9

What synthesizes Sphingomyelin?

Answer 9

made from sphingosine, which is synthesized by the Golgi apparatus

Question 10

What makes glycolipids?

Answer 10

also made from sphingosine, in the Golgi apparatus

Question 11

What is the behavior of phospholipids in the lipid bilayer?

Answer 11

Can flex, rotate, and are laterally mobile within a leaflet (with regional restrictions)
-Spontaneous flipping between leaflets rare.

Question 12

Flipping of membrane phospholipids is rare, but can happen how?

Answer 12

Flippases recognize non-homogeneity. Scrmbleases grab more randomly and mix things up.

Question 13

Specialized patches of lipids and proteins are present in membranes = Lipid Rafts

Answer 13

3rd type of lipid asymmetry – patches of enriched areas with sphingolipids, cholesterol and certain proteins – form “rafts”. E.g. proteins w/ longer hydrophobic regions found here.

Question 14

Membrane Proteins

Answer 14

Alpha-helical strx of transmembrane proteins – due to lack of h2o in transmembrane region, prot h-bonds w/ itself forming helical strx.

Beta-barrels are “integral membrane” proteins; very strongly bound within.

Peripheral prot’s are more easily removed; are on both sides.

Question 15

How can peripheral proteins become anchored?

Answer 15

Add lipid group (purple squiggly tails in figure from slide). Can also have GPI anchors – oligosaccharide protein linked to anchored lipid on external surface.

Question 16

_______, a heavily glycosylated membrane region, acts as a proctection barrier for cells. Also serve in cell identification due to variety of sugar moieties.

Where do membrane proteins get glycosylated?

Answer 16

Glycocalyx.

glycosylation occurs in ER on lumen side.

After being packaged and exported from ER, sugars face out from cell membrane.

Question 17

______ can bind to both intra and extracellular material. They function in both adhesion and signaling and are common in epithelial cells.

Epithelial cancers often ignore signals that detachment has occurred. This is an example of inside-out or outside-in signaling.

Answer 17

Integrins

outside-in signaling occurs in epithelial cancers. integrins’ int’x w extracellular stuff due to changes in integrin reactions with intracellular components.

Question 18

______ links protein in RBC’s. In most cells ______ does this.

Answer 18

Spectrin in RBC’s is like filamentous actin in other cells

Question 19

_______ is a large integral membrane protein that self-associates in the presence of calcium ions. It is an important adhesive molecule, linking cells together that express the same type of cadherin (different types of cadherins adhere cells together in tissue-specific patterns).

Answer 19

Cadherin

Question 20

SER

Answer 20

SER –lipid synthesis, Ca++ regulation, detoxification

Question 21

RER

Answer 21

Protein Synthesis, but generally not cytosolic proteins. They’re made in ribosomes not on RER.

Question 22

What determines whether a polyribosome becomes attached to an ER membrane or remains free-floating in the cytoplasm?

Answer 22

Signal sequence binds to signal recognition particle. Receptors are in ER for signal rec partical and becomes bound to membrane of RER.

Question 23

Protein translocator

Answer 23

ID’s PP & forms pores, opens laterally to release prot’s into plane of membrane. Different integral membrane proteins associate differently in terms of what faces cytosol/lumen.

Question 24

Integral protein introduction to membranes

Answer 24

piptidase clips protein which ends up in lumen. Chaperone proteins help this process by associating w/ them and help pull them into lumen as well as aiding proper folding. …lots of misfoldings can occur  basis of lots of diseases; Alzheimer’s. ER has a robust system for detecting misfolded proteins. What determines single pass, multipass and what faces which direction? Signal sequence in PP itself. These sequences binds in a specific way to translocator protein. Orientation determines what faces where. # of sequences det # of passes. Upon completion, translocator has to release protein to membrane of ER…right

Question 25

Glycosylation of intermembrane proteins?

Answer 25

**Glycosylation** Assembled initially on lipid molecule **dolichol** on **ER membrane**. *Transferred to Asn residue via N-linked glycosylation*. Can have multiple or just one Asn residue glycosylated. *Process begins on cytosolic side, but is completed on lumen side*. **Most** glycosylated proteins are **N-linked**, but also a limited amount of **O-linked glycosylation: linked w/ Ser or Thr; heavy O-linked glycosylation in proteoglycans done in golgi**.

Question 26

Proteoglycans

Answer 26

special class of very heavily glycosylated proteins. The protein core of a proteoglycan is made in the ER, but glycosylation (via an O-linkage) occurs either in the Golgi apparatus or outside the cell by enzyme complexes embedded in the plasma membrane. glycosaminoglycans are added one at a time, by specific glycosyl transferases. Sugars are usually sulfated and negatively charged, which attract cations and water, leading to the formation of hydrated gels.

Question 27

Glycoprotein Comparisons

Answer 27

_Proteoglycans_: ***O**-linked **glycosylated** in G**o**lgi or outside cell Up to **95% carbohydrate by weight** Highly **charged** GAGs typically about **80 sugars long*** _Other glycoproteins_: *N-linked **Glycosylated in ER** and modified in Golgi Usually **only a few % carbohydrate by weight** Numerous **short**, branched oligosaccharide **chains***

Question 28

Protein Synthesis - Quality Control

Answer 28

CHAPERONES help nascent proteins fold correctly (present in both cytoplasm and ER). Misfolded proteins are ubiquinated (in cytosol) and destroyed by PROTEASOMES (in cytosol). **Misfolded ER proteins are retrotranslocated into the cytoplasm by a membrane** **translocase complex** for ubiquitylation and disposal. Misfolded proteins are destroyed. System is proteasomes. Also destroy normal proteins that cells need to get rid of. Where are proteasomes? Cytoplasm. Thus, target proteins need to leave ER. Chaperones (like ubiquitin) help. Glycanases trim off sugars. Proteins are tagged w/ ubiquitin (in cytosol) to be recognized and destroyed by proteasome. Cystic fibrosis; slightly misfolded, but still functional Cl- transporter. System recognizes it and destroys it….even though its functional.

Question 29

\_\_\_\_\_\_\_\_\_ is believed to be the primary cause of Alzheimer's disease, Parkinson's disease, Huntington's disease, Creutzfeldt-Jakob disease, cystic fibrosis, Gaucher's disease and many other degenerative and neurodegenerative disorders

Answer 29

Protein misfolding

Question 30

Different ways cells address accumulation of misfolded proteins

Answer 30

If in **cytoplasm**, called **Heat-Schock response**. Misfolded in **ER**; **Unfolded Protein Response**. Don’t memorize differences, but know 3 mechanisms of detection and response: IRE1 – a *kinase that recognizes misfolded proteins and phosphorylates itself and acts as a splicing machine splicing out mRNA and stimulates chaperone production to correct misfoldings*. PERK – *Increases chaperone prod & inhibits translation factors (decrease prot synth to reduce load on ER)*. & ATF6 – Involves *protein that itself acts as a transcription factor regulating proteolysis and stimulates chaperone production to help.*

Question 31

OTHER FUNCTIONS OF ENDOPLASMIC RETICULUM: Lipid synthesis, Ca++ regulation and detoxification

Question 32

Lipid Synthesis

Answer 32

**Phospholipids** and **cholesterol** are **synthesized by ER enzymes that have their active sites facing the cytoplasm**; scramblases equilibrate lipids between the bilayer leaflets Ceremide is made by ER, transported to Golgi and used to make glycolipids and sphingomyelin

Question 33

True false, Cells normally keep cytosolic Ca++ levels high

Answer 33

False, cytosolic Ca++ levels are kept very low. ER membranes possess Ca++ transporters that actively transport Ca++ into ER lumen...(can pump back out w/ other transporters if necessary, though)

Question 34

Detoxification

Answer 34

Most occurs in **SER** (less in RER) Carried out by **cytochrome p450** family of enzymes These **enzymes render foreign compounds more hydrophilic so they can be released into the bloodstream and eliminated by the kidneys**

Question 35

Sanfilippo syndrome

Answer 35

an example of compromised lysosome function

Question 36

Membrane Trafficing

Answer 36

A central feature of ER, Golgi and lysosome functioning is the formation and transport of membrane-bound vesicles, in concert with the ability of the plasma membrane to bring into, and release material from, the cell by the processes of endocytosis and exocytosis. ## Footnote Numerous prominent medical issues are known to result from specific perturbations in the functioning of these organelles.

Question 37

Golgi Apparatus: Which side is cis FACE? trans?

Answer 37

Just downstream of ER. “pancake” flattened sacks interconnected to tubules and vesicles. Modify proteins. Proteins get to golgi from ER via budding off vesicles. On opposite side of golgi, vesicles pinch off. Cis – ER side; trans – exit side. Different sides have different enzymes; proteins are SEQUENTIALLY MODIFIED as they enter and leave golgi. [![]()](https://s3.amazonaws.com/brainscape-prod/system/cm/049/212/275/a_image_thumb.jpg?1378435173)

Question 38

Golgi Function

Answer 38

Receives lipid and protein products from the ER Returns 'escaped' proteins that should be resident in ER Modifies glycoproteins (both trimming and addition) Sulfation and other post-translational modifications Glycolipid and sphingomyelin production Adds O-linked oligosaccharides to proteoglycans

Question 39

'Post-office' of the cell: directs material to be transported further along 3 primary routes: - Lysosomes - Secretory vesicles - Plasma membrane

Answer 39

[![]()](https://s3.amazonaws.com/brainscape-prod/system/cm/049/215/441/a_image_thumb.png?1378435446)

Question 40

What’s “fuzzy coat” on membranes?

Answer 40

Fuzzy coats are protein coats that facilitate vesicle formation and transfer between sites. Clathrin: plasma membrane to golgi. COP1: golgi to ER (reverse path). COPII: ER to golgi (fwd path) Why have reverse path? Some proteins that should stay in ER accidentally leave. COP1 brings ‘em back. [![]()](https://s3.amazonaws.com/brainscape-prod/system/cm/049/215/600/a_image_thumb.jpg?1378435669)

Question 41

Formation of COP1 and COPII vesicles involves what process when binding?

Answer 41

Lots of different G proteins that act like switches depending if they are bound to GDP or GTP. Active when bound to latter. Removal of GDP and exchange for GTP turns on. Other enzymes hydrolyze GTP --\> GDP. **COPII** proteins have **Sar-1, a small G protein**. Binds to membrane and activates and rcruits other adaptor and cargo proteins which concentrates the cargo and curve the membrane. Other prot’s recruited, vesicle buds off to move to golgi (again, COPII example).

Question 42

What ID’s returning proteins?

Answer 42

KDEL proteins innate in ER proteins remains in these when they accidentally are exported. Upon return, KDEL receptors in ER recognize they belong. [![]()](https://s3.amazonaws.com/brainscape-prod/system/cm/049/216/809/a_image_thumb.jpg?1378436257)

Question 43

What mechanisms determine where vesicles go, and how do they fuse with their appropriate targets?

Answer 43

**Rabs** (small family of GTP-binding proteins) serve as identifiers and determine what’s appropriate to bind with. **Snares** facilitate membrane fusion. **V-snares** are long integral membrane proteins **associated w/ vesicles**. **T-snares** are **associated w/ target membranes.** Also, the lipid content of membranes (i.e. phosphatidylinositols) is a critical identifier in determining where vesicles form and fuse

Question 44

Major function of the Golgi

Answer 44

1) oligosaccharide processing of N-linked glycoproteins made in the ER 2) Addition of mannose-6-phosphate on lysosomal enzymes

Question 45

True or false, packaged "goods" leaving golgi for exocytosis are signal dependent.

Answer 45

False. This is the default pathway. Goods sorted to lysosomes and those Sorted to secretory granules require specific signals

Question 46

Lysosomes. What determines if something should be sent here? Where do enzymes come from?

Answer 46

Digestive organ of the cell...are endosomes until enzymes hydrolases from golgi arrive to lower pH Specific **glycosylated oligosaccharides** ID if something should be sent to lysosomes. Older parts of organelles are often sent to lysosomes (autophage). Also, external content taken in by **phagocytosis** (large scale) and via **endocytosis** (more specifically) **can be fused w/ lysosomes**. Hydrolytic **enzymes** **come from golg**i. When are these active? Low pH. *Hence, these hydrolases are relatively inactive until they get to lysosomes.*

Question 47

What lowers pH in endosome?

Answer 47

Proton pumps.

Question 48

Endocytosis

Answer 48

[![]()](https://s3.amazonaws.com/brainscape-prod/system/cm/049/221/370/a_image_thumb.jpg?1378437409) Note that uncoating of clathrin coat occurs before fusing with early endosome

Question 49

How are lysosomal acid hydrolases packaged and delivered to endosomes?

Answer 49

Cis-Golgi: a mannose-6-phosphate (M6P) 'tag' is added to lysosomal acid hydrolases Trans-Golgi: receptors for M6P concentrate lysosomal enzymes into vesicles, which bud off of the Golgi and fuse with early endosomes. [![]()](https://s3.amazonaws.com/brainscape-prod/system/cm/049/221/684/a_image_thumb.jpg?1378437688)

Question 50

Endocytotic vesicles can appear to be 'coated' or 'uncoated.'

Answer 50

**Coated** endocytotic vesicles contain **clathrin** as a **transient** peripheral membrane protein Many **uncoated** vesicles contain **caveolin** as a **permanent** integral membrane protein. Caveolin are associated w/ signal transduction events and uptake of materials

Question 51

What actually helps endocytotic vesicle pinch off of vesicle? What removes clathrin coat?

Answer 51

**Dynamin**: protein that helps clathrin-coated transport vesicle **"bud" off from membrane** Uncoating **ATPases** (Hsp70 family) **remove clathrin coat,** which is recycled

Question 52

Exocytosis occurs these two ways:

Answer 52

Constitutive secretory pathway (unregulated) Regulated secretory pathway (Ca++ often trigger near secretory vesicles; mast cells have lots)

Question 53

Review of Vesicular Trafficking and Membrane Flow

Answer 53

Prominent types of coat proteins involved in vesicular trafficking: \*COPI – *Golgi to ER* \*COPII – *ER to Golgi* \*Clathrin – *endocytosis*, *Golgi to endosomes/lysosomes* Recognition of vesicle and target membranes and membrane fusion mediated by: \*Rab proteins \*Effector proteins \*SNAREs In addition to these pathways, another pathway exists that is able to move material across cells – **transcytosis**.

Question 54

Mitochondrial morphology

Answer 54

Mitochondria tend to localize along microtubules and can establish close connections with the ER

Question 55

Mitochondrial location

Answer 55

tend to localize to sites of high ATP utilization. Examples include numerous mitochondria aligned along the contractile myofibers in cardiac muscle, and a spiral array of mitochondria around the highly motile sperm tail (flagellum).

Question 56

Mitochondrial plasticity

Answer 56

highly dynamic, and continually undergo fission and fusion. Regions of continuous, extensively branched arrays

Question 57

How are nuclear-encoded cytosolic mitochondrial proteins recognized and imported into mitochondria?

Answer 57

**Shape** (alpha-helical strx) is what routes them into mito. **TOMs** transport outer --\> inner membrane. *Or***,** TOMs transport all the way **into matrix by int’x w/ TIMs**. **OXA** located in inner membrane and transports mito-made proteins out.

Question 58

Mitochondrial biogenesis - lipid

Answer 58

Instead of membrane flow, ER lipids can get plucked out and placed in mito outer membrane

Question 59

Peroxisomes

Answer 59

Single membrane bound ## Footnote involved in a variety of **oxidation** reactions, including the production and **removal** of **H2O2**. Contain high concentrations of enzymes. **Detoxification reactions** (e.g., oxidation of ethanol to acetaldehyde) **\*\*\*Beta-oxidation of fatty acids into acetyl CoA**\*\*\* Formation of myelin phospholipids Peroxisomes appear to be produced through a hybrid process of budding from the ER, followed by import of peroxisomal proteins made by free ribosomes in the cytoplasm and fission. Peroxisomal proteins possess a three-amino acid import signal at their C-terminal end, and are imported into the peroxisome by translocator complexes. Defects in peroxisomal protein import and function is particularly damaging to the brain, liver, and kidneys, and is fatal shortly after birth.

Question 60

Nucleus

Answer 60

Nucleus – 2 membranes with pores and lamina. Histones enter in thru pores, rna out. Space b/w inner and outer membranes is continuous w/ ER in places. \*\*The nuclear matrix is a filamentous scaffolding made up of lamins and other less well-characterized proteins and RNA\*\*.--thought to provide sites of attachment for specific spots along chromosomes; this attachment appears to be dynamic, and can help regulate gene expression.

Question 61

Chromosomes

Answer 61

Function of centromeres – segregation to each daughter cell so they can be identical. Euchromatin – noncondensed –active. What crx nucleolus? ***\*\*\*Nuclear org region--\> ribosomal rna***. Ribosomal protein made in cytosol brought in and join together. Chromosomes tend ot occupy "territories"

Question 62

In periodic chormosome attachment to the nuclear matrix, _____ tend to be hot spots for topoisomerase activity.

Answer 62

MARs MARs intx w/ scaffolding, appear ev 50K-200K nt pairs contain mult small genes, *not big enough to contain large genes*. Loops function independently from neighboring loops – e**xample of higher level of gene expression**. Also thought MARs are **hot spots for topo’s – to resolve torsional problems**. Drugs let topo’s cut, but not repair.

Question 63

\_\_\_\_\_\_ are another correlate of higher level expression in EK chromosomes

Answer 63

relocation to gene “neighborhoods”, away from heterochromatic regions, and to inactive regions to quiet expression.

Question 64

Nucleolus

Answer 64

the ribosome producing factory ## Footnote The most obvious nuclear structure visible is the nucleolus. The nucleolus is a large aggregate of macromolecules, including: rRNA genes Precursor rRNAs Mature rRNAs rRNA processing enzymes ribosomal proteins partially assembled ribosomes

Question 65

How do nuclear products such as mRNAs and ribosomal subunits exit the nucleus? How do nuclear proteins such as histones and transcription factors enter the nucleus?

Answer 65

Nuclear pores are **permeable to small molecules (5000 daltons or less)** *w/o any restrictions*, *even if charged*. **\>60K daltons needs to be recognized and actively transported.** N*ucleoporins form 8 arrays/ring-like strx.* *Filaments* may *help intx w/ transported cmpds*

Question 66

What determines directionality of nuclear imports and exports?

Answer 66

\*\*Imported proteins: Bind import Ran receptors in the presence of GDP, and dissociate in the presence of GTP \*\*Exported proteins: Bind export receptors in the presence of GTP, and dissociate in the presence of GDP [![]()](https://s3.amazonaws.com/brainscape-prod/system/cm/049/234/765/a_image_thumb.jpg?1378440784)