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MCB > W15 > Flashcards

W15 Flashcards

1
Q

What forms around the plasma membrane of all eukaryotic cells?

A

Glycocalyx

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1
Q

What are the two varieties of glycosylated protein?

A

Glycoproteins and proteoglycans

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2
Q

Describe how the protein glycosylation patterns of the different blood types are made.

A

A glycosyltransferase adds a N-acetylgalactosamine (GalNAc) to the distal galactose (Gal), B glycosyltransferase adds a Gal instead of GalNAc, the O phenotype has a frameshift mutation in the enzyme so no sugar is added to Gal

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3
Q

How does the structure of B glycosyltransferase differ from A glycosyltransferase?

A

Differs by four amino acids

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4
Q

What determines the D- or L-configuration of a monosaccharide?

A

Orientation of the asymmetric carbon furthest from the ketone group

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5
Q

Describe the ring forms of monosaccharides.

A

Either pyran (six) ring form or furan (five) ring form. Pyran ring is most commonly in the chair conformation as the boat conformation can cause steric crowding

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6
Q

What is a structural isomer?

A

Same chemical formula but atoms arranged in a different order

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7
Q

What is an epimer?

A

Structural isomer which differs at only one asymmetric carbon

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8
Q

What is an anomer?

A

A structural isomer which differs at asymmetric ring carbons

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9
Q

What is an enantiomer?

A

A stereoisomer which differs by its 3D orientation (mirror image)

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10
Q

What are the characteristics of a glycoprotein?

A

Relatively few sugars bound (1-60% CHO) with fewer, shorter, branched sugars than proteoglycans. The glycocalyx is made mainly from glycoproteins

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11
Q

What are the characteristics of a proteoglycan?

A

Many sugars bound in long unbranched chains of glucosaminoglycans (GAGs) made from carboxylated, sulphated, and/or acetylated sugars. Proteoglycans are mainly found in the extracellular matrix and connective tissues including the cornea, bone, and cartilage. They also form huge complexes bound to water and cations, forming gels to act as shock absorbers such as mucins and vitreous humor in the eye

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12
Q

What is aggrecan?

A

The most common proteoglycan in cartilage, made of two proteins and three GAGs: hyaluronic acid, keratin sulphate, and chondroitin sulphate. It occupies a similar volume to a bacterial cell

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13
Q

What is a glycosaminoglycan (GAG)?

A

An unbranched polysaccharide made from repeating disaccharide subunits of modified aldose sugars

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14
Q

How are monosaccharides transferred onto acceptor molecules?

A

Activated by nucleotide mono- or diphosphates to form nucleotide sugars (e.g. UDP-glucose) before being transferred by a glycosyltransferase which only acts on its cognate nucleotide sugar

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15
Q

What are the two ways sugars are bound to proteins?

A

O-linked or N-linked

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16
Q

Describe O-linked glycoproteins.

A

Sugar attached via oxygen of serine or threonine (or hydroxylysine), first sugar is usually N-acetylgalactosamine (GalNAc). In collagen, O-linked sugars are attached to a hydroxylysine.

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17
Q

Describe lysyl hydroxylase.

A

Hydroxylates lysine using vitamin C as a cofactor, vitamin C deficiency leads to unstable collagen hence scurvy

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18
Q

Describe N-linked glycoproteins.

A

Sugars attached via the nitrogen of an asparagine in the sequence Asn-X-Ser/Thr, where X is any aa except proline. N-linked oligosaccharides all have a common core of sugars (14-mer) attached to the initial N-acetylglucosamine (GlcNAc)

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19
Q

How does N-linked glycosylation take place?

A

N-terminal signal sequences direct a protein to the ER translocator. As it is being translocated, oligosaccharyl transferase transfers the 14-mer oligosaccharide from the dolichol phospholipid onto the protein

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20
Q

What are the two classes of N-linked oligosaccharide?

A

High mannose and complex

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21
Q

What is the function of glycosidases?

A

Break glycosidic bonds

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22
Q

What is the function of glycosyltransferases?

A

Form glycosidic bonds

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23
Q

Once the 14-mer oligosaccharide has been transferred to the protein, how does N-linked glycosylation continue?

A

The 14-mer oligosaccharide is processed in the ER and Golgi by glycosyltransferases and glycosidases

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24
Q

How is protein folding controlled by N-linked glycosylation?

A

The glycoprotein terminal glucose binds to the membrane-bound protein calnexin in the ER. Glucosidase cleaves the glycosidic bond, releasing the protein from calnexin, at which point glucosyl transferase binds the protein and verifies it has correctly folded. Correctly folded glycoprotein exits the ER while misfolded protein binds a new glucose via UDP-glucose and the cycle repeats until completely folded

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25
Q

What is the function of Endo H?

A

Cleaves the glycosidic bond between the two proximal N-acetylglucosamines that begin the oligosaccharide extension

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26
Q

What characterises an endo H resistant glycoprotein?

A

Glycoprotein which binds a terminal GlcNAc, preventing endo H from cleaving the glycosidic bond between proximal N-acetylglucosamines

27
Q

In E.coli, which enzyme performs strand resection of homologous recombination?

A

RecBCD

28
Q

In E.coli, what enzyme performs homology search and strand exchange of homologous recombination?

A

RecA

29
Q

In E.coli, what enzyme performs Holliday junction migration of homologous recombination?

A

RuvA and RuvB (form a helicase)

30
Q

In E.coli, what enzyme performs Holliday junction resolution?

A

RuvC (nuclease)

31
Q

In the RecBCD complex, what provides the nuclease activity in homologous recombination?

A

RecC

32
Q

In the RecBCD complex, what provides the ATP-dependent helicase activity in homologous recombination?

A

RecB and RecD

33
Q

What is the name of the short sequence that halts nuclease activity on the 3’ end at a dsDNA break in homologous recombination?

A

Chi site

34
Q

How many nucleotides can a single RecA protein bind in each DNA binding site?

A

Three nucleotides

35
Q

Describe RuvA found in homologous recombination.

A

A tetramer Holliday junction specific binding protein

36
Q

Describe RuvB found in homologous recombination.

A

An ATP-dependent dsDNA helicase hexamer, one RuvB hexamer binds each heteroduplex

37
Q

Describe RuvC of homologous recombination.

A

A dimer endonuclease specific to Holliday junctions, a dimer binds each Holliday junction symmetrically and cuts strands (with same sequence) opposite each other

38
Q

What is different about homologous recombination at a collapsed replication fork?

A

Collapsed replication fork produces a single-end dsDNA break hence there is only one Holliday junction

39
Q

What nuclease performs dsDNA breaks in programmed homologous recombination?

A

Spo11

40
Q

What nuclease performs end resection in programmed homologous recombination?

A

MRX

41
Q

Define gene conversion.

A

The nonreciprocal transfer of genetic material from one homologous chromosome to another

42
Q

Define loss of heterozygosity.

A

A genetic event that can occur in the dividing cells of a diploid organism heterozygous for one or more markers, in which a daughter cell becomes homozygous or hemizygous for one or more alleles through mitotic recombination, deletion, or gene conversion

43
Q

Name the four main protease classes.

A

Serine proteases, cysteine proteases, aspartic proteases, and metalloproteases

44
Q

How do serine proteases hydrolyse peptide bonds?

A

Asp raises the pKa of His, enabling His to attract a proton from Ser, generating a reactive alkoxide ion which hydrolyses a peptide bond via nucleophilic attack

45
Q

Name the five major families of intracellular proteases.

A

Caspases, cathepsins, calpains, pro-protein convertases, and the proteasome

46
Q

What are the two major protein degradation pathways?

A

Lysosomal and ubiquitin-mediated

47
Q

What are the four routes of substrate protein delivery to the lysosome?

A

Endocytosis, autophagy, phagocytosis, and chaperone-mediated autophagy

48
Q

Acid hydrolases are transported to the lysosome when tagged with M6P in the Golgi, what are the two-steps of this tagging process?

A

In the cis-Golgi, the lysosomal hydrolase signal patch bind GlcNAc phosphotransferase. GlcNAc phosphotransferase adds GlcNAc-Pi to the terminal mannose of the N-linked oligosaccharide via UDP-GlcNAc. Next, a phosphodiesterase removes the GlcNAc, leaving M6P tagged to the acid hydrolase

49
Q

How does an M6P tagged acid hydrolase get transported to the lysosome?

A

M6P binds to a M6P receptor in the TGN, before a clathrin-coated vesicle transports to an early endosome which transports to the lysosome. As the pH drops, M6P-tagged acid hydrolase dissociates from the receptor and a retromer coat recycles the M6P receptor back to the TGN

50
Q

How do lysosomal storage diseases develop?

A

Mutations in GlcNAc phosphotransferase prevent acid hydrolase transport to the lysosome hence substrate degradation does not take place, forming inclusion bodies

51
Q

Describe ubiquitin.

A

Small highly conserved protein with exposed lysine residues on its surface, including Lys48. It forms isopeptide bonds with its C-terminal carboxylate and a substrate Lys residue

52
Q

How is polyubiquitin formed?

A

Isopeptide bond between C-terminus and Lys48 of another ubiquitin

53
Q

How many ubiquitin are required in polyubiquitin to mark a protein for degradation?

A

Minimum of four ubiquitin

54
Q

Name the three enzymes involved in activating ubiquitin.

A

E1: ubiquitin-activating enzyme, E2: ubiquitin-conjugating enzyme, E3: ubiquitin ligase

55
Q

What is the function of ubiquitin-activating enzyme (E1)?

A

E1 Cysteine residue forms a thioester bond with ubiquitin C-terminus, requiring ATP (producing AMP) before binding to E2

56
Q

What is the function of ubiquitin-conjugating enzyme (E2)?

A

Shuttles ubiquitin from E1 Cys to its own Cys, allowing E1 to dissociate

57
Q

What is the function of ubiquitin ligase enzyme (E3)?

A

E3 binds the protein substrate and catalyses the formation of an isopeptide bond, E2 is in complex with E3 so holds ubiquitin in close proximity

58
Q

What are the three routes E3 can become activated?

A

Phosphorylation by a protein kinase, ligand binding, and protein subunit addition

59
Q

What are the three routes a substrate protein can be marked to associate with E3?

A

Phosphorylation by a protein kinase, unmasking of a recognition site, and removal of N-terminal residues

60
Q

Describe the structure of the proteasome.

A

The central 20S catalytic core contains four rings, two with 7 alpha subunits that sit either side of the two rings with 7 beta subunits. Either side of the catalytic core is a 19S cap

61
Q

Describe the catalytic activity of the 20S catalytic core of the proteasome.

A

Only the beta1, beta2, and beta5 subunits of each ring are active. N-terminal threonine of the beta subunit causes nucleophilic attack to cleave peptide bonds, producing peptides of 7-9 residues

62
Q

Describe the activity of the 19S caps of the proteasome.

A

Recognise the polyubiquitinated proteins, isopeptidase releases the polyubiquitin and unfolds the protein using many ATP, the unfolded protein is fed through the central cavity to the catalytic core

63
Q

How are misfolded proteins transported from the ER to the proteasome?

A

Chaperone proteins identify the misfolded protein and prevent aggregation via hydrophobic effect. Disulphide isomerase reduces disulphide bonds to unfold the protein. A lectin recognises the oligosaccharide and binds. The protein translocator complex recognises the lectin-oligosaccharide complex and allows passage into the cytosol. E3 ubiquitin ligase of the translocator complex adds polyubiquitin to the protein, preventing backsliding back into the ER. AAA-ATPase pumps the protein into the cytosol. N-glycanase removes the oligosaccharide en bloc before transport to the proteasome marked by polyubiquitin (joined via Lys48)

64
Q

Why is the catalytic activity of the proteasome unique?

A

It is the only threonine protease

65
Q

What does the drug Velcade (bortizomib) do?

A

Binds to the active site of beta5 in the proteasome, inhibiting activity so pro-apoptotic signals are upregulated in myeloma cells

MCB (10 decks)

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