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From Flashcardlet > Molecules to Cells New Stuff for Exam 1 > Flashcards

Molecules to Cells New Stuff for Exam 1 Flashcards

0
Q

What does it mean if a fatty acid chain is unsaturated?

A

it contains one or more double bonds and has a branched structure

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1
Q

What are fatty acids?

A

Carboxylic acids composed of a hydrocarbon chain

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2
Q

What does it mean when a fatty acid chain is fully saturated?

A

It contains no double bonds and has a linear, unbranched structure

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3
Q

Double bonds in fatty acids occurring in nature usually occur in what configuration?

A

cis

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4
Q

Triacylglycerol contains a single _______ molecule linked to three _________ (each in an ______ linkage to ______)

A

glycerol, fatty acids, ester, glycerol

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5
Q

Lipases release _________ from ________.

A

fatty acids, adipocytes

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6
Q

What phospholipid is abundant in mitochondria and are important for mitochondrial energy metabolism?

A

Cardiolipin

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7
Q

What is the deficiency that causes Barth Syndrome?

A

Deficiency in cardiolipin –> decreased mitochondrial production –> cardiomyopathy, general weakness

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8
Q

Phosphatidylserine is enriched in which monolayer of the lipid membrane?

A

Inner layer

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9
Q

What subset of phospholipids are found in lipid bilayers?

A

Glycerophospholipids

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10
Q

Similar to triacylglycerols, phospholipids are constructed on a glycerol backbone except there is a _______ at C3 instead of a third fatty acid.

A

phosphate

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11
Q

______________ is the parent compound from which other phospholipids can from be synthesized by modification of the ________ group (this one has a -H there).

A

Phosphatidic acid, phosphate

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12
Q

All phospholipids have a net _______ charge at pH 7 except for PE and PC

A

negative

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13
Q

Phospholipids contain 2 _______, one ______, and one ______

A

fatty acid chains, glycerol, phosphate (that can be modified)

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14
Q

The hydrocarbon attached at C1 on a phospholipid is usually ________

A

saturated

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15
Q

The hydrocarbon attached at C2 on a phospholipid is usually ________

A

unsaturated

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16
Q

What is the starting material for phosphatidic acid synthesis?

A

Glycerol-3-phosphate

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17
Q

Fatty acids like phosphatidic acid can be incorporated into _________ for the storage of metabolic energy

A

triacylglycerols

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18
Q

What is the major precursor of glycerol-3-phosphate?

A

dihydroxyacetone phosphate

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19
Q

What are the two steps that are required to make triacylglycerol from phosphatidic acid?

A

1) a phosphatase removes the phosphate –> DAG (diacylglycerol)
2) acyl transferase adds a fatty acid chain –> triacylglycerol

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20
Q

For what purpose would phosphatidic acid be converted to triacylglycerol?

A

For storage of metabolic energy

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21
Q

What are the two alternative pathways for phosphatidic acid synthesis?

A

1) phosphorylation of DAG by DAG kinase

2) hydrolysis of phosphatidylcholine by phospholipase D

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22
Q

What molecule supplies the phosphate group to synthesize phosphatidates/phospholipids?

A

CDP

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23
Q

Pulmonary surfactant functions to reduce ______________ in lung alveoli, thereby decreasing their tendency to ______ during expiration.

A

surface tension, collapse

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24
Q

What is the deficiency in neonatal respiratory distress syndrome?

A

Deficiency in surfactant

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25
Q

What cells secrete surfactant?

A

Type II epithelial cells in lungs

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26
Q

In normal cells, phosphatidylserine is exposed to the ________ of the membrane bilayer, but in a apoptosing cell, the orientation changes, and it is now exposed to the ________ of the cell, signaling to other molecules that the cell is dying.

A

inner layer, outside

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27
Q

_________ A1 removes a fatty acid chain from the C1 position in a phospholipid, and _________ A2 removes a fatty acid chain from the C2 position in a phospholipid

A

phospholipase, phospholipase

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28
Q

Why is phospholipase A2 particularly important?

A

Because it can release arachidonic acid from the C2 position of phospholipids which is used to synthesize eicosanoids (paracrine hormones)

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29
Q

What enzyme cleaves the C3 phosphodiester of phospholipids to make DAG?

A

phospholipase C

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30
Q

How does phospholipase C contribute to cell signaling?

A

1) Phospholipase C cleaves PIP2 into DAG and IP3
2) DAG has two fatty acid chains in it, so it will stay in the membrane, while IP3 is soluble and will trigger the release of Ca2+ from the ER
3) Ca2+ and DAG will activate protein kinase C to phosphorylate downstream substrates–>signaling cascade

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31
Q

What would phospholipase C and D do to a protein with a GPI achor in the lipid bilayer?

A

They would cleave the anchor and release the protein from the cell

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32
Q

GPI anchors anchor ________ proteins to the ________ layer of the lipid bilayer and are attached to the proteins on the ______ terminal residue.

A

extracellular, outer, carboxyl

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33
Q

What are ether phospholipids?

A

a subclass of phospholipids that have an ether linkage at the C1 carbon instead of an ester linkage

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34
Q

What is the structure of platelet-activating factor?

A

It is an ether phospholipid and has one ether-linked long chain fatty acid and an acetyl ester instead of three fatty acids.

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35
Q

Why is platelet-activating factor (PAF) clinically important?

A

By interacting with different receptors, PAF:

  • mediates hypersensitivity and anaphylactic shock
  • triggers the release of serotonin (a vasoconstrictor) from platelets
  • stimulates smooth muscle contraction
  • is involved in Late Phase Reaction
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36
Q

Sphingolipids have a _______ backbone instead of a _________ backbone like glycerophospholipids.

A

sphingosine, glycerol

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37
Q

Sphingolipids can be found in most _______, but are particularly abundant in cells of the __________.

A

membranes, central nervous system

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38
Q

What kind of molecule is sphingosine?

A

An amino alcohol

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39
Q

What sphingolipid compound is the base of all other sphingolipids?

A

ceramide, which has an -H as a head group

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40
Q

Which sphingolipid is a phospholipid?

A

sphingomyelin

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41
Q

What is sphingomyelin?

A

It is a sphingolipid that is the chief component of myelin, the membranous sheath that surrounds and insulates the axons of some neurons. Its polar head is phosphocholine or phosphoethanolamine.

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42
Q

Glycosphingolipids: if it has one polar carbohydrate head group attached to the hydroxyl group of ceramide, it is a _________, and if there is more than one carbohydrate groups attached then it is a _______.

A

cerebroside, globoside

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43
Q

Gangliosides are glycolipids that are _______ charged because they have a carbohydrate head group called __________, a sialic acid. These are a type of _________ and are highly abundant in ________.

A

negatively, N-acetylneuraminic acid (Neu5Ac), sphingolipid, the brain

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44
Q

Phospholipids and sphingolipids are degraded in _________.

A

lysosomes

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45
Q

In order to degrade a glycolipid (like a ganglioside), you need _______ to degrade the _______ portions.

A

exoglycosidases, carbohydrate

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46
Q

How are exoglycosidases named?

A

By the carbohydrate they remove (ex: galactosidase removes galactose)

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47
Q

What are sphingolipidoses?

A

Lysosomal storage diseases where there is an abnormal accumulation of sphingolipids

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48
Q

What is Tay-Sachs disease?

A

It is a lysosomal storage disease where there is a deficiency of hexominidase A (exoglycosidase) which leads to the accumulation of GM2 in the lysosome –> neurological defects in children

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49
Q

What happens in Neimann-Pick disease?

A

Deficiency of sphingomyelinase which leads to the accumulation of sphingomyelin in the lysosome –> neurological defects in children

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50
Q

What do patients with sphingolipidoses usually exhibit?

A

neurological defects

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51
Q

Which class of fatty acids function as hormones?

A

eicosanoids

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52
Q

Eicosanoids are _________ derivatives that are __________ and have a variety of effects on human tissues and cells (e.g., ______________, ________________, ______________, ________________, ______________).

A

fatty acid, short-lived, reproductive function, inflammation, fever and pain associated with injury or disease, formation of blood clots, regulation of blood pressure

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53
Q

What kind of hormones are eicosanoids? Explain.

A

Eicosanoids are a family of paracrine hormones (they act short-range). They interact with G-protein coupled receptors (GPCRs) on target cell surface.

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54
Q

What are the three types of eicosanoids and what is their common precursor?

A

prostaglandins, thromboxanes, and leukotrienes; all eicosanoids are synthesized from arachidonic acid

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55
Q

What are the distinguishing structural differences between the three eicosanoid types?

A

prostaglandins have 5-membered rings, thromboxanes have 6 membered rings, and leukotrienes have no ring but have three double bonds in series (hence TRIene) and four double bonds total

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56
Q

We cannot convert oleate into arachidonic acid, we need ________ (an ________), which we get from ________.

A

linoleic acid, essential fatty acid, food

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57
Q

Cleavage of membrane phospholipids by __________ releases arachidonic acid, the precursor to _________.

A

phospholipase A2, eicosanoids

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58
Q

Big picture for eicosanoids: we get ___________ from our diet –> membrane phospholipids store ____________ –> _____________ releases __________ –> ____________ is converted to _______/_______/________ –> exert _______ hormonal effects

A

linoleic acid, arachidonic acid, phospholipase A2, archidonic acid, prostagladins, thromboxanes, leukotrienes, paracrine

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59
Q

What is the central enzyme in prostaglandin and thromboxane synthesis from arachidonic acid?

A

COX (bifunctional enzyme cyclooxygenase, aka prostaglandin H2 synthase)

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60
Q

What are the two activities of the COX enzyme? What is the purpose of this enzyme?

A

cyclooxygenase, peroxidase; converting arachidonic acid to prostaglandins and thromboxanes

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61
Q

What additional enzyme other than COX is needed to convert arachidonic acid to thromboxanes? Where is this enzyme found in abundance? What is the ultimate goal of this conversion?

A

thromboxane synthase, in platelets, to make the 5-membered ring to a 6-membered ring

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62
Q

What enzyme is needed to convert arachidonic acid to leukotrienes? What does this enzyme require? What does the enzyme do? Where is it found?

A

Lipoxygenases, iron, adds peroxide group, heart, lung, brain, spleen

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63
Q

What is prednisone and what does it do?

A

It is a corticosteroid, it is an inhibitor of eicosanoid synthesis. It inhibits COX-2 synthesis and also inhibits phospholipase A2 from releasing arachidonic acid from phospholipids. In this way it inhibits the production of all three kinds of eicosanoids.

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64
Q

What are the two main groups of eicosanoid inhibitors?

A

Corticosteroids, non-steroidal anti-inflammatory drugs (NSAIDS)

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65
Q

What are two major NSAIDs? How do NSAIDs work?

A

Aspirin, ibuprofen. NSAIDs inhibit the cyclooxygenase activity of COX and therefore inhibit prostaglandin and thromboxane synthesis.

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66
Q

Why does taking a low dose of aspirin on a regular basis decrease the risk of heart attack and stroke?

A

Because aspirin is a NSAID, which inhibit thromboxane synthesis. One of thromboxane’s functions is to induce platelet aggregation.

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67
Q

Why can COX inhibitors cause stomach irritation?

A

COX-1 generates prostaglandins that regulate the secretion of gastric mucins, glycoproteins that protect the gastric lining. which are highly glycosylated proteins of the gastric mucosa. Inhibition of COX-1 can result in the undesired side effect of stomach irritation

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68
Q

In phospholipids, C1 and C2 are _______, and C3 is ________.

A

hydrophobic, hydrophilic

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69
Q

What is the difference between the two COX isoforms?

A

COX-1 is constitutively expressed in many tissues, whereas COX-2 generally has inducible expression

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70
Q

What are two COX-2 specific inhibitors and what was the problem with them?

A

Vioxx and Celebrex, increased risk of heart attack and stroke

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71
Q

Leukotrienes are a type of ______. Several leukotrienes have pro-inflammatory effects mediated through ________. Elevated levels of certain leukotrienes are associated with ______ and _____ (e.g., some leukotrienes induce contraction of the ______ muscle lining the _____________, thereby increasing _______).

A

eicosanoid, G-protein coupled receptors, asthma, anaphylactic shock, smooth, airways of the lungs, bronchoconstriction

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72
Q

What amino acids only have one codon?

A

Met (methionene) and Trp (tryptophan)

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73
Q

tRNAs have an ______ sequence that is complementary to the ______ sequence on ______

A

anticodon, codon, mRNA

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74
Q

What are the ribosomal units for prokaryotic and eukaryotic ribosomes?

A 
70S = 30S + 50S
80 = 60S + 40S
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75
Q

What are the three termination codons?

A

UAA, UAG, UGA

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76
Q

What is the difference between missense mutations and nonsense mutations?

A

Missense mutations encode for the wrong amino acid, nonsense mutations encode for a termination codon

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77
Q

The aligment of the codon (in _____) and anticodon (in _____) is ______.

A

mRNA, tRNA, antiparallel

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78
Q

Binding between tRNA anticodons and codons: mRNA is read _______ by a _______ anticodon

A

5’ to 3’, flipped

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79
Q

Wobble Hypothesis: tRNAs can recognize more than one codon for a specific amino acid due to a ‘wobble’ at the ___ end of the ___________, forming non-traditional base pairs.

A

5’, tRNA anticodon

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80
Q

Anticodons of nonsense suppressor tRNAs have been mutated such that they ___________________________.

A

incorporate an amino acid at termination codons (i.e., they suppress the normal termination of a protein)

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81
Q

Explain degeneracy.

A

The genetic code is resistant to mutation due to degeneracy. Degenerate code allows certain mutations to still code
for the same amino acid.

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82
Q

What enzyme catalyzes the activation of amino acids?

A

aminoacyl-tRNA synthetase

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83
Q

What is the second genetic code?

A

aminoacyl-tRNA synthetases are specific for both amino acid and tRNA, and matching each amino acid for the correct tRNA can be viewed as the “second genetic code”

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84
Q

Prokaryotes produce ______ mRNAs; eukaryotes produce _______ mRNAs.

A

polycistronic, monocistronic

monocistronic: mRNA contains the genetic information to translate only a single polypeptide
polycistronic: mRNA carries several open reading frames (ORFs), each of which is translated into a polypeptide

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85
Q

In prokaryotes, the ________ is involved in the correct positioning of the ribosome at the translation start site and it binds to the _____ of the mRNA, which is ______ of the translation start site.

A

16S rRNA (RNA component of the ribosome), Shine Delgarno sequence, upstream

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86
Q

In prokaryotes, ______ is the first amino acid in a peptide; in eukaryotes, it is ______.

A

F-methionene, methionene

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87
Q

In prokaryotes, _____ inserts N-formylmethionene.

A

initiation tRNA

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88
Q

All organisms have two ___________.

A

tRNAs for Met

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89
Q

Some asthma medications target the _________ pathway.

A

leukotriene

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90
Q

Cholesterol serves as the precursor for the synthesis of ______, _______, and ______.

In contrast to what is found in the serum, most cholesterol in cellular membranes occurs in a _______, ________ form. Cholesterol is a ______ lipid, with an extensive nonpolar region containing ___________, and a
small polar region (i.e., the _________).

A

steroid hormones, bile acids, vitamin D, free, unesterified, amphipatic, 4 fused rings, hydroxyl group

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91
Q

Cells tightly regulate the amount of _________ cholesterol to regulate __________, with excess cholesterol being _______ and packaged as lipid droplets inside cells.

A

unesterified, membrane rigidity, esterified

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92
Q

How is cholesterol transported in the body?

A

In lipoprotein particles (LDL, HDL), surrounded by a phospholipid monolayer and plasma lipoproteins like Apo B-100, with triacylglycerols, as cholesteryl esters

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93
Q

Outline the cholesterol biosynthesis pathway.

A

acetate –> mevalonate –> activated isoprene –> squalene –> cholesterol

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94
Q

What enzyme carries out the rate-limiting step for cholersterol biosynthesis, and what does it convert into what?

A

HMG-CoA reductase, takes HMG-CoA to mevalonate

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95
Q

What are statins?

A

Statins such as lipitor are competitive inhibitors of HMG-CoA reductase and blocks the de novo synthesis of cholesterol to lower serum levels.

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96
Q

What is the most common protein modification?

A

Glycosylation

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97
Q

Carbohydrates are _______ and their C1 is called _______/________. They spontaneously form _________________, and the alpha anomer has a __________ group ________ the plane of the ring and the beta anomer has it _________.

A

polyhydroxyl aldehydes, asymmetric, anomeric, cyclic hemiacetals, hydroxyl, below, above

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98
Q

Oligosaccharides are polymers containing 2 or more monosaccharides joined together by ___________ linkages, ex: ______, which is a polymer of _______.

A

O-glycosidic, glycogen, glucose

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99
Q

Which carbohydrates are found predominantly in glycosaminoglycans?

A

xylose, glucuronic acid, iduronic acid

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100
Q

What is the mechanism to activate sugars and make them into nucleotide sugars?

A

nucleoside triphosphate + sugar 1-phosphate –> nucleoside diphosphate + phosphate

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101
Q

What is classic galactosemia?

A

Caused by deficiency of GALT; accumulation of galactose and galactose-1-phosphate –> failure to thrive, hepatomegaly, jaundice, cataracts. Treatment is elimination of galactose and lactose from the diet.

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102
Q

What is the substrate for glycogen synthase?

A

UDP-glucose

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103
Q

Glucuronyltransferases are important in _______ synthesis, ________, ________, and ________. Their substrate is ________.

A

glycoprotein, drug detoxification, excretion of steroid hormones, heme metabolism, UDP-glucuronic acid

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104
Q

Glycosyltransferases mediate the following reaction:

______/_______ carbon of one sugar becomes glycosidically bonded to the _______ group of the acceptor

A

C1, anomeric, hydroxyl

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105
Q

Where are N-glycosidic linkages made?

A

Between asparagine and N-acetylglucosamine, within a triplet of Asn-X-Ser/Thr

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106
Q

Biosynthesis of N-linked oligosaccharides:
1. Preassembly of a oligosaccharide chain attached to _________, a membrane-associated lipid.
Mevalonic acid serves as the precursor of ______, as well as cholesterol. Therefore the regulation of ______ synthesis is directly related to cholesterol metabolism.

A

dolichol phosphate (dol-P)

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107
Q

________ catalyzes the co-translational transfer of the 14 residue oligosaccharide chain from ________ to the _____ residue in certain _________ sequences of growing polypeptide chains.

A

Oligosaccharyltransferase (OST), dol-P (lipid-linked intermediate), Asn, Asn-X-Ser(Thr)

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108
Q

Synthesis of Oligosaccharide-Dol-P: 14 different glycosyltransferases, 1st 7 steps occur _________, last 7 steps occur ________.

A

on cytosolic face of RER, in lumen of RER

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109
Q

The active site of oligosaccharyltransferase is _________.

A

Inside the lumen of the ER

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110
Q

Initial Glc3Man9GlcNAc2 structure can be changed or processed by the action of _________ and _________ as the glycoprotein moves through the ______ and ______.

A

glycosyltransferases, glycosidases, ER, Golgi

111
Q

Why start all N-glycosylation with Glc3Man9GlcNAc2 structure in the ER if the action of glycosidases (ER & Golgi) and
glycosyltransferases (Golgi) will change this structure?

A

Because this structure is part of an elaborate quality control mechanism found in the ER, where chaperones can sense by sensing that carbohydrate structure whether a protein is folded or not. It’s utilizing that particular structure in that particular glycan to know whether or not the protein is folded.

112
Q

What are proteoglycans?

A

Glycoproteins that contain a specific type of oligosaccharide/carbohydrate chain on them called glycosaminoglycans

113
Q

Proteoglycans are found in the _________, they are associated with ______ and they are very highly glycosylated (can have as many as 100 _________ chains “bottle brushes”)

A

extracellular matrix, collagens, glycosaminoglycan

114
Q

Glycosaminoglycans are ______ charged ______ composed of repeating _______ units (______ + _______) which can be _____; large capacity to __________.

A

negatively, polysaccharides, disaccharide, amino sugar, uronic acid, sulfated, bind water

115
Q

Name the four glycosaminoglycans.

A

hyaluronic acid, chondroitin sulfate, heparin and heparin sulfate, dermatan sulfate

116
Q

What is hyaluronic acid, and what is special about it?

A

It is a glycosaminoglycan but it is not covalently linked to protein and it is not sulfated. It provides scaffold for proteoglycans in extracellular matrix.

117
Q

Mucins are heavily __________ glycoproteins found in mucous secretions or on the cell surface

A

O-glycosylated

118
Q

What is Cancer Antigen 125?

A

It is an antigen found on Muc16 that is highly elevated in ovarian cancer patients and is therefore used as a marker for the diagnosis of ovarian cancer. A decline in serum levels of CA125 is associated with a response to therapy.

119
Q

What is erythropoietin?

A

Erythropoietin is a glycoprotein growth factor secreted by the kidney which stimulates the production of red blood cells. When there is reduced oxygen levels in the body, the kidney secretes erythropoietin, which then stimulates the red bone marrow to enhance erythropoiesis.

120
Q

Erythropoietin contains 3 ________ oligosaccharides. Without these, the protein only exhibits 10% activity.

A

N-linked

121
Q

What is heparin and how does it work?

A

Heparin is a glycosaminoglycan anticoagulant. It activates antithrombin upon binding, which then inhibits procoagulant proteases, factor 10A and thrombin, thereby decreasing the production of fibrin clots.

122
Q

_________ can be injected into joints to treat osteoarthritis, because it is a ________, which can _________ and ______ the joint.

A

Hyaluronic acid, glycosaminoglycan, bind water, lubricate

123
Q

Each blood type has its own _______at make specific ________ on the RBC surface.

A

glycosyltransferases, oligosaccharides

124
Q

What is glycation?

A

It is a non-enzymatic process that generates glycosylated proteins. Diabetes patients have high amounts of glycated hemoglobin.

125
Q

Why are glycated proteins bad?

A

They can undergo further structural changes to generate Advanced Glycation End Products (AGEs) that can cross-link other proteins and damage them.

126
Q

How does hemoglobin get glycated?

A

Glucose becomes covalently attached to ε-amino groups of lysine residues in hemoglobin

127
Q

Why is glycosylation important in influenza virus infections?

A

Influenza has HA (hemagglutinin) on its surface which recognizes sialic acid on host glycolipids and glycoproteins as cell surface receptors and uses them to enter into the cell.

128
Q

What are tamiflu and relenza?

A

They are sialic acid analogs that are designed to slow the inluenza virus from infecting host cells

129
Q

Catabolism of glycolipids, glycoproteins, and proteoglycans occurs in the _______. Their carbohydrate units are degraded _________ by ___________ solely from the _________ end of the oligosaccharide.

A

lysosomes, sequentially, exoglycosidases, nonreducing

130
Q

What enzyme is necessary for hydroxylation of prolines in collagen?

A

prolyl 4-hydroxylase

131
Q

Acetylation gets rid of ______ charges on ______-charged amino acids.

A

positive

132
Q

What is a “rheostat”?

A

It is the ability of different patterns of phosphorylation to modulate the activity of an enzyme.

133
Q

What is Hutchinson-Gilford progeria?

A

Premature aging disease that is characterized by accumulation of prelamin A, which is farnesylated.

134
Q

Where do all proteins start their synthesis?

A

On ribosomes free in the cytosol

135
Q

What types of proteins are synthesized on ribosomes on the ER?

A

Secretory proteins (water soluble) and transmembrane proteins

136
Q

Where do proteins that finish being translated on the cytosolic ribsosomes end up?

A

In the cytosol, mitochondria, nucleus, peroxisomes

137
Q

What is the role of the signal recognition particle? What is its structure?

A

It is a ribonucleoprotein composed of RNA and 6 polypeptide chains. It binds to the signal sequence on the nascent growing polypeptide chain that is being synthesized on a free ribosome and also binds to the ER membrane. Binding of SRP momentarily stops translation.

138
Q

Signal sequence has a ______ structure and is usually found on the ______ terminus of a protein. The three parts of a signal sequence are a ______ amino-terminal domain which contains a net ______ charge, a _______ core domain that typically forms a _______, and a ______ carboxyl-terminal domain. Signal sequences that are found on the _____ are cleaved co-translationally by _______.

A

tripartate, amino, hydrophilic, positive, hydrophobic, alpha helix, polar, amino terminus, signal peptidase

139
Q

All signal sequences adopt similar ________.

A

three-dimsensional conformation

140
Q

SRP receptor is only found on _______, and its SRP binding site is exposed to the _______. It will only bind _______________.

A

ER, cytosol, SRP/nascent polypeptide chain/ribosome complex

141
Q

Where do secretory proteins go once they are translocated on the ER surface?

A

ER lumen

142
Q

Translocation, or ______ into _______, requires _________ and occurs through an aqueous pore or channel called ______. _____ is also involved in this process.

A

import, the lumen of the ER, ATP hydrolysis, translocon, GTP

143
Q

Translocation and ________ are usually coupled since ________ are the preferred substrate for translocation.

A

protein synthesis, unfolded polypeptide chains

144
Q

Translocated polypeptide chains fold into their native conformation in _________ with assistance of _______.

A

the lumen of the ER, chaperones

145
Q

What is a stop-transfer sequences?

A

Hydrophobic, alpha-helical sequences which function to anchor the protein in the membrane. Proteins that span the membrane many times contain numerous stop-transfer sequences.

146
Q

Some integral membrane proteins do not have a _______, they only have ______ that keeps them in the membrane of the ER.

A

signal sequence, stop-transfer sequences

147
Q

If a protein has an N-linked carbohydrate on it, if it’s a proteoglycan, it has to get to the ______ in order to get those modifications.

A

secretory pathway/ER

148
Q

The ____ part of the Golgi is closest to the ER, and the ____ part of the Golgi is farthest from the ER.

A

cis, trans

149
Q

It is in the _______ where proteins are sorted to go to either the plasma membrane, to be stored in _________ or ________ until the cell gets a signal, or they can be delivered to the _______.

A

trans Golgi network, secretory vesicles, granules, lysosome

150
Q

The _______ secretory pathway is common to all cells.

A

constitutive

151
Q

What is the “default” secretory pathway?

A

The constitutive secretory pathway, which brings proteins to the surface. If it’s a water soluble protein, it will be secreted. If it’s an integral membrane protein, it will associate with the plasma membrane.

152
Q

In some cells, such as exocrine cells, endocrine cells, and neurons, the _______ secretory pathway is present in addition to the _____ secretory pathway, and a subset of secretory proteins are sorted to ________ from which they are released only upon stimulation of the cell. Two examples of this are _____ and _____.

A

regulated, constitutive, secretory granules, insulin, neurotransmitters

153
Q

How do we get soluble enzymes into lysosomes?

A

Soluble acid hydrolases are tagged with mannose-6-phosphate (phosphorylated sugar) on N-glycans, which directs their delivery to lysosomes by mannose-6-phosphate receptors. These proteins are brought to endosomes and ultimately go to the lysosome.

154
Q

Lysosomes contain ______ enzymes that are _____ soluble and are also called _______. These are optimally active near pH ___.

A

hydroyltic, water, acid hydrolases, 5

155
Q

How are lysosomes acidified?

A

Membrane V-type ATPases hydrolyze ATP and pumps protons into the lysosome.

156
Q

Lysosomes are _____ centers.

A

recycling

157
Q

What are the three pathways to the lysosome?

A

Phagocytosis (macrophage), endocytosis, autophagy

158
Q

What is autophagy and basal autophagy?

A

Autophagy is “self-eating,” where a cell can engulf other organelles or other molecules in the cytosol and then break down those molecules. Basal autophagy is a routine housekeeping function in the cell, quality control mechanism (get rid of dead mitochondria for example).

159
Q

When is autophagy upregulated?

A

Starvation

160
Q

What enzyme recognizes acid hydrolases that need to go to the lysosome to start modifying them with the necessary modifications? What is the first modification?

A

N-acetylglucosamine phosphotransferase adds a N-acetylglucosamine and a phosphate onto a mannose residue

161
Q

What is the “uncovering enzyme?”

A

It is the enzyme responsible for the second step in modifying acid hydrolases that are targeted for the lysosome, and they are N-acetylglucosaminidases which removes N-acetylglucosamine and you’re left with a phosphorylated mannose.

162
Q

What is mucolipidosis II (I-cell disease)?

A

Defect in N-acetylglucoasmine phosphotransferase, you don’t put the necessary tag on the acid hydrolases that need to go to the lysosome, so the enzymes are secreted!! You do not have a functional lysosome!

163
Q

Vesicular transport between organelles involves:

1) a ______-covered vesicle buds from a donor compartment
2) _______ are released from the vesicle
3) the _____ vesicle binds to a specific target compartment
4) fusion of the ______ vesicle to the target membrane

A

coat protein, coat proteins, uncoated, uncoated

164
Q

What proteins mediate vesicles fusing with a particular target compartment?

A

SNARE proteins

165
Q

Explain how a secretory vesicle will get to the cell membrane.

A

The secretory granule has its own unique v-SNARE on it that will only recongnize the t-SNARE on the plasma membrane. SNARE molecules are integral membrane proteins, and they’re going to interact very tightly (like a wench), they bring secretory granule closer to the plasma membrane, and it fuses and releases contents.

166
Q

How do vesicles move in a cell?

A

Along “tracks” of microtubules

167
Q

Tetanus and botulism are made from ___________ whose spores are widely distributed in ______.

A

anaerobic bacteria (Clostridium), soil

168
Q

How do botulinum and tetanus work?

A

They are peptidases that cleave SNARE molecules, botulinum blocks the release of acetylcholine and results in flaccid paralysis, whereas tetanus blocks the release of inhibitory neurotransmitter GABA and results in spastic paralysis (lockjaw)

169
Q

For what conditions is botox used?

A

overactive muscle contraction, back pain, bladder spasms, migraines, incontinence, cerebral palsy

170
Q

Receptor-mediated endocytosis is a ______________ mechanism, receptors are a way to ______ ligands without taking up large amounts of extracellular fluid.

A

selective concentrating, concentrate

171
Q

In receptor-mediated endocytosis, receptors are concentrated in ________.

A

coated pits

172
Q

Receptor mediated endocytosis: go through the steps.

A

1) Receptors are concentrated in coated pits
2) Coated pits become coated vesicles
3) The vesicle uncoats and fuses with an endosome (which is an acidified compartment with V-Type ATPases, endosomes are acidic but not as acidic as lysosomes)

In some cases, vesicles will bud off the endosome and recycle the receptor back to the plasma membrane.

173
Q

What is the structure of clathrin?

A

Clarthrin is a triskelion-shaped protein complex composed of noncovalently associated polypeptide chains (3 heavy and 3 light). These chains undergo self-assembly to form protein “cages”

174
Q

What needs to happen to protein coated vesicles before they fuse to the endosome?

A

clathrin needs to dissociate and return to the cell surface to form a new coated pit.

175
Q

What is the role of clathrin?

A

Clathrin is a protein that helps form the necessary invagination of the plasma membrane to mediate receptor-mediated endocytosis. The clathrin binds the intracellular area (which ultimately becomes the outside of vesicle) where receptors that are favorable to become a part of these pits are concentrated.

176
Q

How is iron taken up by a cell?

A

Receptor-mediated endocytosis

177
Q

Transferrin is a ______ protein

A

water soluble

178
Q

How does transferrin help in the cell’s uptake of iron?

A

Transferrin (a water soluble protein) binds iron and then is bound by the transferrin receptor on the cell surface. Transferrin receptors will preferentially cluster on clathrin-coated pits –> clathrin-coated vesicle –> coat comes off –> vesicle fuses with endosome –> low pH of endosome (pH 6) causes iron to dissociate from transferrin –> iron is released into the cytosol to take part in heme assembly –> apotransferrin (transferrin + transferrin receptor without iron) is brought to the cell surface –> at pH7 in the extracellular environment, transferrin comes off the transferrin receptor

179
Q

How is the transferrin process pH-dependent?

A

Transferrin receptor will only bind transferrin + iron at pH 7 (extracellular), iron will only dissociate from this complex at pH 6 (endosome), and transferrin-without-iron will only fall off the transferrin receptor at pH 7 (extracellular)

180
Q

Mucolipidosis II (I-cell disease) is what kind of disease?

A

Protein targeting and protein modification defect

181
Q

What are the clinical manifestations of familial hypercholerstolemia?

A

Elevated concentration of LDL in the plasma and deposition of LDL-derived cholesterol in tendons and skin (xanthomas) and in arteries (atheromas)

182
Q

What is the inheritance of familial hypercholerstolemia?

A

Is is an autosomal dominant trait with a gene dosage effect (homozygotes are more severely affected than heterozygotes)

183
Q

What is the mutation that causes familial hypercholesterolemia?

A

A mutation that affects the structure and function of the LDL receptor

184
Q

High levels of LDL in plasma are associated with what disease?

A

atherosclerosis

185
Q

How is LDL taken up by the cell?

A

1) LDL receptors on the surface of the cell bind ApoB-100 on the LDL
2) receptors cluster in clathrin coated pits
3) LDL is endocytosed
4) Endosome fuses with a lysosome
5) Lytic enzymes in the lysosome degrade the LDL into amino acids, fatty acids, and cholesterol

186
Q

What does GlcNAc-phosphotransferase do?

A

It targets proteins to the lysosome by adding a mannose-6-phosphate tag

187
Q

Cell-surface receptors are for _______ signal molecules

A

hydrophilic

188
Q

Intracellular receptors are for ______ signal molecules.

A

hydrophobic

189
Q

Hydrophobic signal molecules are brought into the cell by _________.

A

a carrier protein

190
Q

What are the four different types of signal transduction?

A

Contact-dependent, paracrine, synaptic, endocrine

191
Q

What is unique about contact-dependent signaling?

A

The signal molecule is membrane-bound on a signalling cell.

192
Q

What is unique about paracrine signaling?

A

Signaling molecules are produced by the signaling cell, and these molecules can affect many surrounding cells.

193
Q

What is unique about synaptic signaling?

A

It is very fast (neurotransmitter released from a neuron to stimulate target cell)

194
Q

What is endocrine signaling?

A

A signaling molecule (usually a hormone) is released by the endocrine cell and it is carried to target cells in the blood stream. The speed of this signaling is determined by blood flow.

195
Q

What is the difference between fast and slow signal transduction?

A

In fast signal transduction, the proteins in the cytoplasm are modified (ex: phosphorylated), and in slow signal transduction, the signaling goes to the nucleus, and ultimately new proteins that are altered are made.

196
Q

How does nitric oxide stimulate smooth muscle relaxation?

A

An activated nerve cell releases acetylcholine, stimulating endothelial cells to release nitric oxide. Nitric oxide enters the smooth muscle cell, binds guanylyl cylase, which produces GMP which stimulates rapid relaxation.

197
Q

What are nuclear receptors and what do they bind?

A

Nuclear receptors are on the nuclear surface and they bind to hydrophobic signaling molecules (hormones). All nuclear receptors have a DNA binding domain and thus affect transcription.

198
Q

How do nuclear receptors work?

A

Nuclear receptors are usually bound by inhibitory proteins and are in an inactive state. When the ligand binds, there is a conformational change and nuclear translocation of the receptor + ligand is induced. This complex then binds to coactivator proteins to form a transcriptional activation protein complex, and binds to a specific site on the DNA to activate transcription.

199
Q

Name 6 hormones.

A

cortisol, estradiol, vitamin D3, testosterone, thyroxine, and retinoic acid

200
Q

Explain the primary response and secondary response to steroid hormone.

A

Primary: Nuclear receptor + steroid activate transcription of primary response genes which produce primary response proteins.
Secondary: Primary response proteins shuts off their own genes, and activate the transcription of secondary response proteins which then carry out all of the different aspects of cellular processes.

201
Q

What are the three largest classes of cell surface receptors?

A

Ion-channel coupled receptors, G protein coupled receptors, and enzyme-coupled receptors

202
Q

What are the two main types of molecular switches?

A

Phosphorylation and GTP-binding

203
Q

What kind of energy is required for phosphorylation molecular switches?

A

ATP

204
Q

How does the GTP-binding molecular switch work?

A

A protein that has GDP bound to it is usually inactive. A signal will come into the cell and the GDP will be exchanged for a GTP, activating the protein and allowing it to activate other downstream proteins. GTP can be hydrolyzed by the cell (by its own GTPase activity) to turn it off again.

205
Q

What are the two types of GTP-binding proteins?

A

Trimeric (G proteins) and monomeric (small GTPases)

206
Q

What two proteins regulate the activity of monomeric GTP-binding proteins and what does each do?

A

GAPs and GEFs. GAPs increase the rate of GTP hydrolysis, which turns the small GTPase off. GEFs promote the release of bound GDP in exchange for GTP to activate small GTPases.

207
Q

What do scaffold proteins do??

A

Scaffold proteins regulate specificity by aligning different molecular switches in close proximity. When the ligand binds the receptor, the receptor can activate these molecular switches consecutively.

208
Q

How does a receptor become a docking site for other proteins?

A

When a ligand binds, the receptor autophosphorylates its tyrosine kinase domains and generates many phosphotyrosine residues. These attracts different proteins and a transient signaling complex can be formed.

209
Q

How do receptors form docking sites on lipids of the plasma membrane?

A

This requires phosphoinositides. When the receptor becomes activated, phosphoinositides are modified by phosphorylation, and this becomes a docking site for an enzyme and its substrate. The enzyme (an intracellular signaling protein) can then modify its substrate which can lead to activation and downstream signaling.

210
Q

What two domains can recognize phosphorylated tyrosine?

A

SH2 domains and PTB domains

211
Q

What domain binds short proline-rich amino acid sequences?

A

SH3 domains

212
Q

What does SH2 domains bind?

A

Phosphorylated tyrosine

213
Q

What do PTB domains bind?

A

phosphorylated tyrosine

214
Q

What do SH3 domains bind?

A

short proline-rich amino acid sequences

215
Q

What domain binds to charged head groups of specific phosphoinositides?

A

PH domains

216
Q

What do PH domains bind?

A

Charged head groups of specific phosphoinositides.

217
Q

In what cell is positive feedback regulation very important?

A

Muscle cell differentiation; once differentiation is triggered, it does not stop.

218
Q

What does the positive feedback loop do?

A

It sustains signaling even after signal strength drops, this can contribute to making permanent decisions for development (e.g., muscle cell differentiation)

219
Q

What surface receptor is the most commonly targeted by drugs?

A

G-protein coupled receptors

220
Q

What is the structure of GPCRs?

A

A single polypeptide chain with seven transmembrane domains (threads back and forth across the lipid bilayer seven times)

221
Q

How do GPCRs work to activate downstream signaling?

A

GPCRs are bound to G proteins (trimeric, with subunits alpha, beta, gamma). Inactive GPCRs are bound by GDP. When the GPCR is activated, it serves as a GEF, and it exchanges the GDP on the G protein for a GTP, thereby activating the G protein. The activated G protein can then activate different molecular switches.

222
Q

Microtubule structure: Microtubules are hollow cylinders about _____ in diameter. They are composed of ______ and ______, which form ______ that are arranged as ______. The microtubule wall contains ________.

A

25 nm, alpha-, beta-tubulin, heterodimers, protofilaments, 13 protofilaments.

223
Q

What is necessary for microtubule self-assembly?

A

A critical concentration of heterodimers (of alpha- and beta-tubulin), GTP, and a physiological concentration of salts

224
Q

What determines the inherent polarity of microtubules?

A

Different assembly rates of their plus and minus ends, and the fact that the heterodimers are asymmetric.

225
Q

What is an example of the dynamic instability of microtubules in vivo?

A

Rapid assembly and disassembly of the mitotic spindle during mitosis. Spindle microtubules (organized in a polarized pattern) form rapidly during metaphase and depolymerize quickly when cell division is complete.

226
Q

What does dynamic instability mean?

A

It refers to a process in which assembly or disassembly of microtubules is regulated locally (assembly is favored when dimers at the plus end contain bound GTP)

227
Q

How do microtubule-targeting anti-cancer drugs work? What is an example?

A

These drugs interfere with cell division by binding to tubulin and either stabilizing of disrupting microtubules. Taxol stabilizes microtubules, preventing them from depolymerizing at the end of mitosis.

228
Q

What is an MTOC?

A

Microtubule organizing centers, sites where polymerization of microtubules is organized and initiated

229
Q

What is the cell’s principle MTOC?

A

The centrosome, which is located centrally in most cells that contain centrioles

230
Q

What is a centriole?

A

A microtubule based structure consisting of nine triplet microtubules, found in the centrosome and are involved in organization of the mitotic spindle.

231
Q

What are basal bodies?

A

A microtubule based structure consisting of triplet microtubules. These are centrioles that have moved to the cell surface to initiate the formation of cilia.

232
Q

MTOCs establish ___________ of a population of microtubules. The ______ of microtubules are ________ to MTOCs.

A

unform polarity, minus end, adjacent

233
Q

What is gamma tubulin?

A

It is a component of the gamma-tubulin ring complex which is involved in initiation of polymerization of microtubules at MTOCs, and caps the minus end of the microtubule preventing its disassembly. Gamma tubulin does not form tubular structures like alpha and beta tubulin.

234
Q

What are the two microtubule-based organelle and what are their functions?

A

Cilia and flagella. These are found on the cell surface of most eukaryotic cells and in some cases they are motile organelles (cilia of respiratory tract, flagella of spermatozoa) and in some cases they have a sensory function (sensory cilia of the olfactory epithelium, kidney tubules, and photoreceptors).

235
Q

What is an axoneme? What is its structure?

A

It is the cytoskeletal component of cilium or flagellum. It has a highly conserved 9 + 2 pattern of microtubules. The central pair consists of 2 normal microtubules and the 9 outer doublets consist of A and B subfibers. In most sensory cilia the central pair microtubules are missing.

236
Q

If an axoneme is missing its two central microtubules, what is it?

A

A component of sensory cilia.

237
Q

Axonemes arise from ________ that consist of a cross-linked array of _________.

A

basal bodies, 9 triplet microtubules

238
Q

______ and centrioles have the same srtucture. Both can act as ______.

A

Basal bodies, microtubule organizing centers

239
Q

Explain ciliary bending.

A

It is a classic model for microtubule based motility. The molecular motor is dynein, which causes relative sliding between microtubules in the axoneme. Dynein is a large protein complex that uses energy from ATP hydrolysis to move cargo along microtubules

240
Q

What is dynein?

A

A large protein complex that uses energy from ATP hydrolysis to move cargo along microtubules. it also causes relative sliding between microtubules in the axoneme.

241
Q

What motors mediate motility on single cytoplasmic microtubules?

A

A cytoplasmic form of dynein or by another ATPase motor kinesin

242
Q

How are organelles/vesicles transocated in the cell?

A

Cytoplasmic dynein or kinesin can associate with the surface of organlles (i.e., vesicles) and move them along microtubules.

243
Q

Why do motors move unidirectionally on microtubules, and which motor goes in what direction?

A

Because of the inherent polarity of microtubules. Dynein goes from plus to minus, kinesin goes from minus to plus.

244
Q

What are the structural similiarities between dynein and kinesin?

A

The both have two ATPase head domain and are thought to move along microtubules in a cross-bridge cycle. Cross-bridge cycle coupled to ATP hydrolysis results in movement along the microtubule.

245
Q

Where is fast axonal transport of vesicles by microtubules important?

A

In neurons, where it is critical that vesicles generated through synthesis in the cell body be delivered to the synapse and that vesicular components of the synapse be returned to the cell body. Such vesicles become closely associated with microtubules by binding dynein or kinesin.

246
Q

How does fast axonal transport of vesicles work?

A

Microtubules in axons have a uniform polarity with their minus ends at the cell body and their plus ends at the synapse. Transport toward the synapse (anterograde) is mediated by kinesin, and transport away from the synapse to the cell body (retrograde) is mediated by dynein.

247
Q

Microtubules in axons have a uniform polarity with their minus ends at the ________ and their plus ends at the _______. Transport toward the synapse (anterograde) is mediated by ______, and transport away from the synapse to the cell body (retrograde) is mediated by ______.

A

cell body, synapse, kinesin, dynein

248
Q

Intermediate filemants form from ________, microtubules from ________, and actin microfilaments from ________.

A

intermediate fibrous proteins, tubulin heterodimer subunits, globular actin monomers

249
Q

What cradles the nucles and provides mechanical strength to cells?

A

Rope-like intermediate filaments

250
Q

What is essential for cell movement and distribution of components at the cell surface?

A

Actin microfilaments

251
Q

What are the diameters of actin, intermediate filaments, and microtubules?

A

Actin: 5-9 nm
Intermediate filaments: 10 nm
Microtubules: 25 nm

252
Q

What are most abundant in cells under mechanical stress?

A

Intermediate filaments

253
Q

What are intermediate filaments involved in?

A

They are most abundant in cells under mechanical stress, and are involved in desmosomal intercellular junctions

254
Q

What is a good way to distinguish between epithelial, mesenchymal (derived from bone, cartilage, fat, muscle, vascular, or hematopoietic tissues), and neuronal derived tumors?

A

Monospecific intermediate filament antibodies. Breat and GI primary cancers are keratin positive, and sarcomas (mesenchymal origin) are vimentin positive. Desmin positive = muscle

255
Q

What is the defect in Emery-Dreifuss Muscular Dystrophy?

A

An autosomal dominant mutation of the gene encoding lamins A/C

256
Q

What is the cause of epidermolysis bullosa simplex?

A

Genetically defective keratin filaments in skin epithelial cells render them highly susceptible to mechanical rupturing, producing blistering of the skin and secondary infections

257
Q

What is the structure of intermediate filament proteins?

A

They are variable at the N- and C- terminus but have a conserved alpha-helical rod domain in the center. The alpha helix forms a parallel coiled coil homodimer (the alpha helical domains wrap around one another). This is much like two kinesins with their head groups coming together using a coiled coil principle to align the ends of the kinesin molecules.

258
Q

Why are intermediate filaments nonpolarized?

A

The parallel coiled coild are polarized, but then you take the dimers and flip them, and then make antiparallel tetramers. And then you keep doing that, and then you ultimately have a structure where N- and C- terminal ends of the protein are scattered all through the filament.

259
Q

What are the characteristics of intermediate filaments that distinguish them from microtubules?

A

They are mainly structural components, are not dynamic, and not polarized

260
Q

What mediates assembly and disassembly of intermediate filaments?

A

Phosphorylation and dephosphorylation of their subunits.

261
Q

What is G actin?

A

It is an actin monomer that hydrolyzes ATP –> ADP and polymerizes into F actin (flexible actin microfilaments).

262
Q

What is the energy source for microtubule polymerization and actin polymerization?

A

microtubule: GTP
actin: ATP

263
Q

What do microtubules and actin have in common?

A

They both have minus ends and plus ends that allow for treadmilling –> locomotion

264
Q

What is the role of the GTP cap in microtubule treadmilling?

A

Polymerization at the plus end requires bound GTP which is subsequently hydrolyzed to GDP. Dimers are added most efficiently to an end capped with GTP.
When the rate of addition of dimers exceeds the rate of GTP hydrolysis a GTP cap forms, stablilizing the microtubule.

When the addition of dimers slows down –> reduction of GTP–> lose GTP cap, microtubule can disintegrate from the plus end and disappear

265
Q

What is the critical concentration of actin polymerization mean?

A

Free subunit concentration where on and off rates are equal (on one end of the F-actin). This critical concentration is much higher on the plus side than it is on the minus side, which defines the polarity and causes the plus end to be the end where there is more assembly

266
Q

How does a cell limit G actin polymerization?

A

G actin is bound by thymosin beta 4, which inhibits the bound ATP from being hydrolyzed. When profilin binds to the G-actin, the thymosin is released and ATP can be hydrolyzed to form polymers. Once the polymers are at a desirable length, they can be capped on both ends. In muscle, tropomodulin caps the minus end and capping protein caps the plus end –> maintain length.

267
Q

What enzyme acts to sever actin filaments or initiate their breakdown?

A

ADF cofilin

268
Q

How do bacteria and viruses take advantage of actin polymerization?

A

Proteins on their surface can induce actin polymerization producing actin coments (actin polymerization force is so strong that it can actually move the bacteria and viruses inside the cell)

269
Q

What do cytochalasin and phalloidin do?

A

Cytochalasin disrupts F actin –> depolymerization
Phalloidin stabilizes F actin

These drugs are derived from mushrooms

270
Q

What are the four classes of actin binding proteins?

A

Rgeulating, severing, cross-linking, and motor

271
Q

How is clotting mediated by actin?

A

1) When fibrin clot begins to form it binds to surface proteins on platelets (platelet glycoprotein)
2) Platelet glycoprotein becomes associated with filamin
3) Actin filaments polymerize in association with filamin
4) More and more filamins and actin filaments are added on
5) Platelet cytoplasm turns into a gel-like state that is anchored to the fibrin on the outside

272
Q

Most myosine ATPase heads are _____ directed

A

plus end

273
Q

What enzymes move particles along actin filaments?

A

Myosin I and II (myosin ATPase motors)

274
Q

An amino acid is attached at the ___ end of the tRNA

A

3’

From Flashcardlet (20 decks)

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