Mass spectrum_L4

Question 1

Why does genomics do not explain biology complexity?

Answer 1

Biological complexity is not linearly related to the number of genes

Question 2

How can the cells get around the gene limitation?

Answer 2

(1) Post-translational modification(PTM) is the chemical modification of a protein after its translation, existing protein scaffold is added by chemical groups.
(2) They have profound effects on protein function by altering their activity state, localization, turnover, functionality, half-life and interactions with other proteins.
(3) Over 200 different types of PTM, every amino acid can be modified.

Question 3

What amino acids are most commonly modified and what amino acids are not likely modified?

Answer 3

most commonly: aa with hydroxyl group, e.g. serine, threonine and tyrosine
least commonly: glycine, phenyalanine, glutamic acid, histidine and isoleucine

Question 4

What benefits can the post-translational modification bring in?

Answer 4

(1) respond more rapidly to changes in environmental signals, e.g. danger signal, since the protein production does not rely on the central dogma process.
(2) the more the number of modification sites on the protein, the more combination a single protein can give rise to. PTM increases the protein diversity. However, it does not necessarily mean that every PTM protein is possible, some dynamic PTM protein species are predominant. For example, Serine/arginine repetitive matrix protein 2 involved in pre-mRNA splicing weighs 300 kDa, containg 2,752 AA sequence and over 300 phosphorylation sites

Question 5

What is the significance of heavily PTM regions in the histone?

Answer 5

Functional implication: regulate the histone function and messanger DNA transfer

Question 6

What is the key in cell-cell communication?

Answer 6

Glycan-lectin recognition is key to cell-cell communication, specifc interaction is required for both positive and negative interaction: e.g. (+) organ/tissue development; (-) mediated by suagr interaction, many bacteria interfere the cells by sugar interaction

Question 7

What sugar repertoirs do the glycoprotein have?

Answer 7

1. In the mammalian cells, the number of monosaccharides is lower than that of amino acids. Different orientation of hydroxyl group can cause different recognition events, sometimes even profoundly distinct biological reaction.
2. (1) beta-D-glucose
   (2) beta-D-galactose: the difference between the glucose is the hydroxyl group orientation at C4-position
   (3) alpha-D-mannose: the pnly difference between the glucose and mannose is the orientation of the hydroxyl group at C2-position
3. the modification is the addition of N-acetyle group to C2-position, the fundamental difference between the two members in the class is the orientation of the hydroxyl group at C4-position
   (4) alpha-D-N-acetylglucosamine
   (5) alpha-D-N-acetylgalactosamine
4. addition of carboxylic acid at C-1 position and other functional groups, human cells mostly express alpha-D-N-glycolylneuraminic acid, the gene for hydroxyl group is partially deleted.
   (6) alpha-D-N-glycolylneuraminic acid
   (7) alpha-D-N-glycolylglucosamine(the only difference between alpha-D-N-glycolylneuraminic acid is the additional hydroxyl group attached at the C-4 position group)
5. (8) alpha-L-fucose: epimerization of the beta-D-glucose
6. (9) beta-D-xylose: same chemical groups but slightly different arrangment

Question 8

Glycosidic bond formation

Answer 8

the production of glycan from glucose(either in beta or in alpha form depending on the orientation of the hydroxyl group at C-2 position: up-bended is the beta form and down-bended is the alpha form), catalysed by glucotransferase by formation of glycosidic bond and one molecule of water loss per each bond, the reducing end is the C-2 hydroxyl group is dehydrolysed and involved in the glycosidic bond, vice versa

Question 9

What is glycoprotein?

Answer 9

(1) Best characterized of all the glycoconjugates
(2) High proportion of secreted and membrane bound proteins are glycosylated
(3) Diverse functions
(4) the glycans are hydrophilic and the modified proteins tend to favour water environment and therefore face the hydrophilic sides as either secretory protein or membrane protein

Question 10

what are the two forms of glycosylation?

Answer 10

(1) N-glycosylation, sugar linked to amide nitrogen in the side chain of asparagine: Attached to Asn in the consensus sequon …Asn-X-Ser/Thr…where X is any AA except Pro, but not every peptide fitting the sequence is glycosylated, there is always some variation. The N-glycosylation is initiated in ER by en bloc transfer of a pre-formed lipid-anchored conserved glycan. Glycan is added to the end of the nascent protein as it is initially generated from the ribosome.
(2) O-glycosylation, sugar linked to oxygen in the side chain of serine or threonine

Question 11

N-glycan structure?

Answer 11

(1) The N-glycan structure is conserved partially in the mammalian cells, the conserved part is consisted of three mannose and two alpha-D-N-acetylglucosamine. Two alpha-D-N-acetylglucosamine and one mannose form linear polysacchride chain with alpha-D-N-acetylglucosamine at the non-reducing end to interact with the peptide sequence, the other two mannose branch out from the linear backbone
(2) The variable chains braching out from the conserved region at reducing end are named antennae

Question 12

N-glycan biosynthetic process

Answer 12

(1) synthesis of lipid-anchored oligosaccharides in the endoplasmic reticulum
(2) en bloc transfer of the precursor to the protein inside the ER, N-glycan is enzymatically modified by glucosidase and mannosidase
(3) only the correctly folded glycoproteins are released from ER to Golgi Body, N-glycans can assess whether or not the protein is correctly folded or not
(4) processing in the cytosol: initial trimming of the sugar residues, trimming and modification of the branch structure and addition of sugar terminal residues
(5) the modification continues inside the Golgi Body for remodulling of the attached chemical groups, specific residues are cleaved and glycotransferase adds back some other monosaccharides.
(6) secretion/delivery to the plasma membrane, orientation of the glycans towards the watery envoirnment with membrane-anchored domain embedded in the plasma membrane

Question 13

Eukaryotic N-glycan biosynthesis?

Answer 13

3-types
High mannose
hybrid
complex

Question 14

What is the importance of capping group addition?

Answer 14

The capping group tends to be in alpha bond linkage at the end of the antenna which produces kink or bend to complement more to the carbohydrate binding protein and drive the biological processes. Antennae “capped” with sugars such as Fuc and NeuAc to form ligands for specific recognition by lectins

Question 15

What is O-glycosylation?

Answer 15

(1) Occurs on Ser and Thr
(2) No consensus sequence but some “rules” eg nearby proline, tandem repeats of Ser/Thr
(3) Initiated in Golgi by addition of a single sugar - usually GalNAc in mammals

Question 16

What is O-glycosylation?

Answer 16

(1) Occurs on Ser and Thr (hydroxyl amino acids)
(2) No consensus sequence but some “rules” eg nearby proline, tandem repeats of Ser/Thr are more likely to be O-glycosylated
(3) Initiated in Golgi after full folding by addition of a single sugar - usually GalNAc in mammals
(4) Unlike N-glycosylation, no pre-formed precursor is required
(5) With more O-glycosylation being discovered, the glycan structure is gradually revealed.

Question 17

classes of O-glycans which are classified by the core structure

Answer 17

(1) At least 8 cores known
(2) Cores 1 & 2 very common in glycoproteins in general
(3) Cores 1-4 are the most common on mucins
(4) similarly, the beta-bonded antenna is added, followed by the capping group
(5) NOT elongated to more complex structures.
(6) Localized to the cytoplasm and nucleus: occur in cytoplasmic/nuclear protein or cytoskeleton/mitochondrial protein
(7) Present in all higher eukaryotes studied: the glycan is extended in a specific manner
(8) As abundant as phosphorylation;
(9) O-GlcNAc proteins are also Phosphoproteins
(10) O-GlcNAc and Phosphorylation are often reciprocal.
(11) Highly dynamic modification - a regulatory role: interplay of glycosylation and phosphorylation dictate many functions such as polymerase II activity, close relationship between glycosylation and phosphorylation, many glycosylated sites are all phosphorylated sites

Question 18

What are mucins?

Answer 18

(1) Mucins are cell surface and excreted glycoproteins
(2) Protect mucus membranes by keeping them hydrated, acting as lubricants and prevent invasion by micro-organisms(have protective role: the mucines secreted in the GI tract in respiratory sytem)
(3) Heavy O-glycosylation occurs as a result of multiple S/T tandem repeats