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Foundations 110 > Lecture 5 > Flashcards

Lecture 5 Flashcards

1
Q

Another mode of post-transcriptional gene regulation has been discovered that involves small double-stranded RNA

A

RNA interference

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2
Q

Mammalian cells normally express short double-stranded RNAs, termed microRNA (about 500 different miRNA), that are involved in –.

A

gene silencing

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3
Q

– are important during development, for example to silence particular genes and allow proper differentiation of specific cell types

A

MicroRNAs

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4
Q

– can also be introduced into cells to silence a targeted gene. This allows an easy method to turn off expression of a specific gene. Such “targeted” RNAi has therapeutic potential to treat diseases such as cancer and infection by RNA viruses such as HIV

A

Exogenous double-stranded RNA

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5
Q

There are four basic components of RNAi – the RNA, two processing –, and the RNA-induced Silencing Complex (RISC) that actually carries out silencing

A

RNases

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6
Q

Endogenous microRNA is synthesized as part of a longer RNA by –. The microRNA sequences are homologous and base-pair, forming a “stem” in the precursor.

A

RNA pol II

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7
Q

Two RNases, one in the nucleus and one in the cytoplasm, cleave the – to produce the short (21-25 nucleotide) double-stranded RNA

A

precursor

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8
Q

the cleaved RNA is unwound and one strand associates with an– which is part RISC

A

Argonaut protein,

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9
Q

The single-stranded microRNA targets – to mRNA that contain homologous sequences by base-pairing.

A

RISC

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10
Q

Protein production from the mRNA is prevented either by –or by RISC-mediated inhibition of mRNA translation. RNAi can also inhibit transcription, but the mechanism has not been defined.

A

mRNA degradation

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11
Q

The new technique CRISPR/Cas9 allows changes to be precisely made in –

A

genomic DNA.

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12
Q

Using this technique, nucleotides can be inserted, deleted, or changed in the genome

A

CRISPR/Cas9

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13
Q

CRISPR/Cas9 , it allows targeted mutation of specific genes or sequences, such as those that cause cancer, or – of inherited or somatic mutations that cause disease

A

repair

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14
Q

CRISPR

A

clustered regularly interspaced short palindromic repeats

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15
Q

CRISPR ) refers to arrays of – found in bacteria that play a role in defending bacteria against invasion by viruses

A

repeated sequences

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16
Q

Within CRISPR repeats are sequences – to sequences in bacteria viral DNA.

A

homologous

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17
Q

RNA transcribed from the CRISPR sequences (and processed) binds to – and targets that nuclease to invading viral DNA by base-pairing.

A

a Cas (CRISPR-associated) nuclease

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18
Q

the CRISPR system has been adapted to modify mammalian genomes using a specific version of the Cas nuclease, –, and an engineered guide RNA that consists of sequences homologous to the target sequence and sequences that bind to Cas9.

A

Cas9

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19
Q

Expression of the – and Cas9 in a cell directs the nuclease to sequences in the genome that are homologous with the guide RNA.

A

guide RNA

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20
Q

Once the guide RNA base-pairs, the Cas9 nuclease can – This can cause a deletion, and inactivate the gene

A

cleave both strands of the DNA.

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21
Q

However, if a synthetic DNA strand homologous to the targeted region is introduced, this DNA is used to – the cleaved genome DNA.

A

repair

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22
Q

If the synthetic DNA contains a slightly different sequence, the new sequence is – into the genome.

A

inserted

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23
Q

Eukaryotic cells are organized into membranous compartments (–) that have unique components and functions.

A

organelles

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24
Q

Two important interconnected membrane systems involved in – are the secretory pathway and the endocytic pathway.

A

protein transport

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25
Q

The secretory pathway consists of the – and Golgi complex.

A

endoplasmic reticulum (ER)

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26
Q

The secretory pathway is responsible for transport of –proteins to the appropriate compartment:

A

newly-synthesized

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27
Q

Secretory pathway transports proteins – (e.g. peptide hormone and growth factors such as insulin and epidermal growth factor, components of the extracellular matrix such as collagen, carrier proteins in the blood such as albumin, etc.)

A

out of the cell

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28
Q

secretory pathway transports plasma membrane proteins to the – (e.g. ion channels, hormone receptors, transporters)

A

cell surface

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29
Q

T/F: secretory pathway transports proteins to lysosomes (degradative enzymes of lysosome)

A

true

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30
Q

transporting proteins to secretory pathway organelles (e.g. – and glycosidases in ER and Golgi).

A

glycosylases

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31
Q

The endocytic pathway consists of –(early and late) and ends at the lysosome.

A

endosomes

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32
Q

The endocytic pathway is involved in uptake of material from the – and the extracellular fluid. It is important for uptake of nutrients such as cholesterol and iron, as well as internalization of signaling receptors.

A

plasma membrane

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33
Q

This pathway is also used by certain pathogens such as viruses to enter the cell

A

endocytic pathway

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34
Q

Extensive network of interconnected membrane sacs and tubule

A

endoplasmic reticulum

35
Q

Smooth ER – a major site of – synthesis

A

fatty acid and lipid

36
Q

Rough ER – studded with ribosomes, site of – that enter the secretory pw (also some lipid synthesis) and protein glycosylation.

A

protein synthesis

37
Q

Golgi complex – complex organelle with both – regions and stacked membrane disk called cisternae

A

tubulated

38
Q

Organized into cis Golgi network (closest to ER), –, and trans Golgi network (closest to PM).

A

cis, medial and trans Golgi cisternae

39
Q

Golgi is a site of protein glycosylation and – side chains. Also major site of protein sorting.

A

modification of carbohydrate

40
Q

First step in protein transport through secretory pathway: protein synthesis and – across (or into) ER membrane.

A

translocation

41
Q

Second step in protein transport through secretory pathway: – and modification in ER

A

Protein folding

42
Q

Third step in protein transport through secretory pathway: Transport to Golgi, lysosomes, plasma membrane by budding and –

A

fusion of small transport vesicles.

43
Q

All proteins except those made in the mitochondria are synthesized on –

A

cytoplasmic ribosomes.

44
Q

Proteins are targeted to membrane organelles by –

A

sorting signals

45
Q

Targeting relies on a short stretch of – in the nascent polypeptide that directs it to the appropriate compartment. Referred to as a sorting signal because it is responsible for sorting to a specific compartment.

A

amino acids

46
Q

In the case of ER targeting, the sorting signal is –

A

signal sequence

47
Q

Signal sequence is normally located at the – of the protein and consists of one or more positivelycharged amino acids followed by 6-12 hydrophobic amino acids

A

N-terminus

48
Q

Signal sequence is recognized by –

A

Signal Recognition Particle (SRP)

49
Q

SRP is an – with one RNA and multiple polypeptides

A

ribonucleoprotein particle

50
Q

SRP binds to the large ribosomal subunit and the signal sequence as emerges from ribosome, –

A

pauses translation.

51
Q

SRP-ribosome-nascent polypeptide complex is then bound by–, an ER membrane protein.

A

SRP receptor

52
Q

Both SRP and SRP receptor are – – GTP binding by both increases affinity of SRP for SR.

A

GTPases

53
Q

Once bound to SRP receptor, the ribosome and nascent chain are transferred to the –, a protein that forms a gated channel through the ER membrane.

A

translocon

54
Q

SRP and SRP receptor hydrolyze GTP and –

A

dissociate.

55
Q

Continued protein synthesis pushes the polypeptide in an unfolded state through the translocon channel into the lumen of the ER. The signal sequence is cleaved by a –during translocation

A

protease

56
Q

Newly synthesized membrane proteins integrate into the ER from the translocon.
Same basic process but a –within the protein is transferred to the membrane from the translocon, resulting in an integral membrane protein

A

hydrophobic sequence

57
Q

N-linked glycosylation in the ER.
Proteins undergo N-linked glycosylation during translocation and –, including formation of disulfide bonds, in the lumen of the ER.

A

fold

58
Q

Glycosylation involves the addition of a preformed 14 sugar oligosaccharide from a – donor that is embedded in the ER membrane through the lipid (dolichol).

A

lipid linked

59
Q

The sugar is transferred in block as the target amino acid sequence (asparagine –X – serine/threonine) emerges from the translocon. This – is conserved in all eukaryotic species.

A

“core” oligosaccharide

60
Q

Core is trimmed by – in the ER.

A

glycosidases

61
Q

Folded, glycosylated proteins are transported from the ER to the Golgi by transport vesicles that bud from the ER and fuse with the –.

A

cis Golgi network

62
Q

Many other transport steps in the secretory pathway are mediated by –

A

transport vesicles

63
Q

Vesicles also mediate transport through the –.

A

endocytic pathway

64
Q

Best characterized vesicle transport pathways involve vesicle with protein coats – referred to as –

A

coated vesicles

65
Q

Coat formation: polymerization of specific proteins onto the cytoplasmic face of the organelle membrane forms a “coat” that drives – and collects proteins (cargo) for transport to the next compartment.

A

membrane curvature

66
Q

Sorting signals (normally 4-6aa in length) on the – of cargo bind to coat proteins, directing the cargo into the forming vesicle.

A

cytoplasmic domains

67
Q

Once the vesicle buds from the donor compartment, the coat is –

A

released (uncoating)

68
Q

(Golgi to ER, intra-Golgi)

A

COPI

69
Q

ER to Golgi

A

COPII

70
Q

Golgi to endosomes; endocytosis

A

clathrin

71
Q

Vesicles are targeted to the correct recipient organelle membrane by two classes of proteins: –

A

tethers and SNARES

72
Q

– provide the initial link between vesicle and target

A

tethers

73
Q

SNARES are integral membrane proteins present on both the vesicle (v-SNARE) and target membrane (t-SNARE) and bind each other to drive –

A

membrane fusion

74
Q

v-SNAREs and t-SNAREs form parallel –bundles that force the vesicle and target membrane together.

A

alpha helical

75
Q

Different sets of tethers and SNAREs used at each transport step, providing – in docking and fusion.

A

specificity

76
Q

Vesicle mediated: After proteins are transported from the ER to the Golgi, –oligosaccharides are modified by glycosidases (cleave sugars) and glycosylases (add sugars).

A

N-linked glycoprotein

77
Q

Vesicle mediated: – is a major site of protein sorting

A

trans Golgi network (TGN)

78
Q

Secreted proteins sorted to constitutive secretory vesicles or, in specialized cells to regulated secretory vesicles or granules (e.g. insulin, glucagon, neurotransmitters, digestive enzymes). Regulated secretory vesicles only fuse to plasma membrane if cell receives the appropriate –

A

extracellular signal.

79
Q

Lysosomal enzymes sorted into –coated vesicles that fuse with endosomes.

A

clathrin

80
Q

Clathrin coats also contain “adaptor complexes” which link clathrin to membrane and bind –

A

cargo

81
Q

A – on N-linked oligosaccharides is the sorting signal on lysosomal enzymes

A

sugar modification

82
Q

Defects in lysosomal enzyme sorting due to mutation of GlcNAC phosphotransferase cause recessive inherited lysosomal storage disease called –

A

I-cell disease.

83
Q

Without –, lysosomal enzymes are not sorted into clathrin coated vesicles at the TGN but are secreted from the cell.

A

M6P

84
Q

in I-cell disease, lysosomes do not contain –of the enzymes used for degrading macromolecules

A

normal levels

Foundations 110 (10 decks)

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