Chembio3

Question 1

What are 4 ways carbohdyrate building blocks can vary

Answer 1

Chirality or position of groups (like glucose vs galactose), charge groups such as carboxylic acids added (eg glucaronic acid) or an amide (a glcnac) or glucosamine OR loss of an OH (xylose)

Question 2

What can these variations on carbohydrates do for the various carbs

Answer 2

carboyxlic acid - can add a charge; groups can add bulk

Question 3

pyranose vs furanose

Answer 3

6 vs 5 member ring - draw both and know alpha and beta for both

Question 4

What are some common conformations and what dictates them

Answer 4

chair confo - and steris orbital overlap etc

Question 5

homo vs heteropolysaccharide

Answer 5

Kind of what soudns like - either can be branched, hetero is repeating pattern of the same

Question 6

Whats a common player (carb) in the ECM

Answer 6

glycosaminoglycan (negative charge - sulfated often - more negative charge means more hydrated or slippery - keratan and heparin (more negative charge also means highly branched)

Question 7

Proteo glycan vs glycoprotein

Answer 7

proteoglycan is a glycosaminoglycan with a small protein portion, a Glycoprotein has a lil carb but not a glycosaminoglycan

Question 8

What is a glycosaminoglycan

Answer 8

a 2 sugar unit consisting of a uronic acid and an amino sugar

Question 9

What are common ways proteins and carbs are linked in glycoproteins

Answer 9

Serien or threonine OH or asparagine as an amide (O linked vs N linked)

Question 10

How are glycolipids formed

Answer 10

covalently bonded to O

Question 11

What roles do oligosaccharides play in reecognition?

Answer 11

a vairety of glyocproteins or glycolipids have this reaching out and are recognized and first binding point in ECM (lectins - things that bind carbs) - BIG for toxins, virus -first step in infection

Question 12

Processive vs non processive synthesis

Answer 12

processive assumes the machinery/enzymes forming it never dissociates from the product during (like DNA RNA -polymerase is attached throughout) - non processing assuming - bind, dissoc and rebinding

Question 13

How are sugars linked together

Answer 13

Need to become an “activated sugar” which means attached to a diphosphate molecule such as UDP or GDP. This is a 2 enzyme process - one that takes the sugar and GTP and releases the activated sugar bound to GDP - then ANOTHER enzyme will link that sugar to another - mechanism same as DNA t4 ligase (GDP a good leaving group

Question 14

Describe glyocprotein synthesis

Answer 14

membrane protein - made in ytoplasme as soon as made - translation stalled - goes to ER - gets extruded there into membrane OR into vesicles where it goes to the golgis gets modulated then to cell membrane

Question 15

How are carbs added to glycoproteins

Answer 15

2 spots - based on flanking sites on amino acids - Generally a whole carb ore is made and bound to dolichal where it will bind to our protein and later glycos will be added later

Question 16

Primary vs secondary metabolism

Answer 16

priamry metabolites are needed - produced in large quantities, and generally conserved while secondary are the opposite - low concentrations - not needed -

Question 17

How are FA’s transferred to synthesis

Answer 17

Use a strong base to transfer - moved around as thioeasters attached to co enzyme A handle the transfer of thio esters is better than the transfer of esters

Question 18

poplyketide vs prenoid subunit

Answer 18

2 vs 5 know how to draw

Question 19

Why is claisen of thioesters more favorable than that of esters

Answer 19

both energetically uphill- thioesters is less; alpha proton of thioesters a lot more acidic

Question 20

Type I vs Type II FA synthesis

Answer 20

Type I - all domains on one mega peptide - connected by a flexible linker (eukaryotes) Type II - all enzymes on different peptides

Question 21

integral vs peripheral membane protein

Answer 21

integral part of membrane - peripheral sensitive to salt - have ionic and charge bound to emmbrane

Question 22

How can you predict membrane protein sequence

Answer 22

string of hydrophobics (especially alpha helices - and typically see TRYPTOPHAN AND TYROSINE at the interface

Question 23

How does phospholipase signalling work?

Answer 23

hydrolysis - cleaage of head groups etc

Question 24

Thioesterase uses which amino acids to cleave FA from ACp

Answer 24

Serine aspartic acidand his

Question 25

sphingo vs phosphoplipid

Answer 25

the N ont eh first FA

Question 26

Why do we care about Kd with enzyme binding

Answer 26

Tells us [] of ligand to get half max binding which is key because tells us how concentration change has an effect on activity (at concentrations around Km - its the largest)

Question 27

Fast vs slow receptros

Answer 27

slow receptors cause transcription - downstream changes, fast cause immediate changes eg muscle contraction

Question 28

Describe how nuke receptors work

Answer 28

They're in the ctyoplasm or nucleus ( not plasma membrane) - binds and often make dimers - or they release a dimer that an bind and become a transcription factor (if not in nucleus might allow it to pass some sort of channel or gate to nucleus to bind)

Question 29

What types of molecules do nuek receptors bind and how does that effect Kd

Answer 29

They bind hydrophobics that can pass through plasma membrane but have Poor solubility in cytoplasm SO they pass but at a low concentration means KD HAS TO BE HIGH

Question 30

GPCR pathway

Answer 30

so bind - then GPCR associates with alpha, beta and gamma subinots - which is a GTPASE (alpha is) this causes it to spit out its GDP and take up GTP which makes it active - alpha dissociates causes downstream effects - it's turned off when GTP hydrolyzed back to GDP

Question 31

Common nuke receptor ligands

Answer 31

steroid hormons like progesterone estrogen , testoesrone etcvitamin D (again hdyrophobicS

Question 32

What can nuke binding to homeobod mean

Answer 32

r enhances the expression of the homeobox b-1 gene (Hoxb-1). Hox genes code for transcription factors that further control cell growth and differentiation (

Question 33

Binding to DNA from nuke receptors how?

Answer 33

zinc fingers - some recogzinie repeating 6 bp sequences etc

Question 34

How do G proteins help tune signal response time

Answer 34

ratio of GAP and GEF - as they accelerate different parts of the signal chain - GEF increases signal output by caralyzing the exchange of GDP for GTP - but GAP accelerates hydrolysis of bound GTP to GDP decreasing signal output

Question 35

How do G proteins help tune signal response time

Answer 35

ratio of GAP and GEF - as they accelerate different parts of the signal chain - GEF increases signal output by caralyzing the exchange of GDP for GTP - but GAP accelerates hydrolysis of bound GTP to GDP decreasing signal output KEY BECAUSE NOT BASED OF RECEPTOR LIGAND KINETICS but is tunable

Question 36

Typical alpha subunit function vs Beta and gamma

Answer 36

So alpha will do more downstream pathways to cause expression changes (eg through, IP3, DAG or cAMP, Beta gamma do quicker changes (usually effecting ion channels)

Question 37

Neutral antagonist vs inverse agaonist vs agonist vs partial

Answer 37

Agonist is full rate, neutral keeps it at the same basal rate, inverse agaonist puts below basal and partial is somerate

Question 38

4 steps in the G protein cycel

Answer 38

agonist binding 1 - 2 G protein coupling and nucleotide exchange 3- activted g protein subunits regulat affector proteins 4- GTP hydrolysis and inactivation of G alpha

Question 39

glucose to mannose

Answer 39

Carbon 2 switch position

Question 40

Glucose to galactose

Answer 40

Carbon 4 swtich position

Question 41

l vs d

Answer 41

flipi everything (DETERMINE by going by the chircal carbon furthest from the anomeric - s is l and d is r..?) All D-sugars have the –OH on the right side and L-sugars have the –OH on the left side

Question 42

glucsose to fucose

Answer 42

go to galactose (carbon 4 switcH) then remove OH off of methyl alcohol

Question 43

glucose to xylose

Answer 43

get rid of methyl alcohol

Question 44

glucose to ribose

Answer 44

get rid of 3 carbon (keep all the directionality the same)

Question 45

Hhow do terpene synthases deal with reactive intermediates

Answer 45

active site positoned in a way H2O can't attack - and generally for these carbocations react them with pi bonding orbitals

Question 46

What amino acids stabilize in FA synth (particularly the reduction steps)

Answer 46

Tyrosine and Lysine

Question 47

homoe vs heterodimer

Answer 47

homo dimers are already together but inhibited binding frees it - can go through pucleur pore - heterodimer - both need binding which allows them to come together and be TF

Question 48

Why did they look at human gut microbiome

Answer 48

human gut microbiome was a good source since the A and B antigen structures are present within the mucins that line the gut wall11. These mucins serve as a barrier to the invasion of gut bacteria, but also serve as points of attachment and a source of nutrition for members of the microbiome. Consequently, some of these bacteria should express glycosidases that cleave the A and B antigen

Question 49

2 enzymes they used (blood paper0

Answer 49

as FpGalNAc deacetylase (FpGalNAcDeAc) and FpGalactosaminidase (FpGalNase)

Question 50

Know what aldol condensation looks like and how to do

Question 51

Protein glycosylation vs glycoprotein

Answer 51

protein glyocsylation is non enzymatic but the lysine interactions with the sugar andattaches where the anomeric carbon alcohol would be

Question 52

how does protein prenylation occur

Answer 52

Protein prenylation involves the transfer of either a farnesyl or a geranylgeranyl moiety to C-terminal cysteine(s) of the target protein. There are three enzymes that carry out prenylation in the cell, farnesyl transferase, Caax protease and geranylgeranyl transferase I.

Question 53

Amino acids relevant in other paper

Answer 53

N165 and N234

Question 54

Know details of the moedling paper

Answer 54

So had RBD (receptor binding domain) - binds ACE2 - genearlly shielded all over by glycans - is camoflougaed otherwise - only binds when up - and this being able to go into the a stable up confirmation is N165 and N234 dependant- they fill in that space - seen by modeling experiments - stability of angles also biolayer inferometry - experiences more angle variation