Chembio3 Flashcards
What are 4 ways carbohdyrate building blocks can vary
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)
What can these variations on carbohydrates do for the various carbs
carboyxlic acid - can add a charge; groups can add bulk
pyranose vs furanose
6 vs 5 member ring - draw both and know alpha and beta for both
What are some common conformations and what dictates them
chair confo - and steris orbital overlap etc
homo vs heteropolysaccharide
Kind of what soudns like - either can be branched, hetero is repeating pattern of the same
Whats a common player (carb) in the ECM
glycosaminoglycan (negative charge - sulfated often - more negative charge means more hydrated or slippery - keratan and heparin (more negative charge also means highly branched)
Proteo glycan vs glycoprotein
proteoglycan is a glycosaminoglycan with a small protein portion, a Glycoprotein has a lil carb but not a glycosaminoglycan
What is a glycosaminoglycan
a 2 sugar unit consisting of a uronic acid and an amino sugar
What are common ways proteins and carbs are linked in glycoproteins
Serien or threonine OH or asparagine as an amide (O linked vs N linked)
How are glycolipids formed
covalently bonded to O
What roles do oligosaccharides play in reecognition?
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
Processive vs non processive synthesis
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
How are sugars linked together
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
Describe glyocprotein synthesis
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
How are carbs added to glycoproteins
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
Primary vs secondary metabolism
priamry metabolites are needed - produced in large quantities, and generally conserved while secondary are the opposite - low concentrations - not needed -
How are FA’s transferred to synthesis
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
poplyketide vs prenoid subunit
2 vs 5 know how to draw
Why is claisen of thioesters more favorable than that of esters
both energetically uphill- thioesters is less; alpha proton of thioesters a lot more acidic
Type I vs Type II FA synthesis
Type I - all domains on one mega peptide - connected by a flexible linker (eukaryotes) Type II - all enzymes on different peptides
integral vs peripheral membane protein
integral part of membrane - peripheral sensitive to salt - have ionic and charge bound to emmbrane
How can you predict membrane protein sequence
string of hydrophobics (especially alpha helices - and typically see TRYPTOPHAN AND TYROSINE at the interface
How does phospholipase signalling work?
hydrolysis - cleaage of head groups etc
Thioesterase uses which amino acids to cleave FA from ACp
Serine aspartic acidand his
sphingo vs phosphoplipid
the N ont eh first FA
Why do we care about Kd with enzyme binding
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)
Fast vs slow receptros
slow receptors cause transcription - downstream changes, fast cause immediate changes eg muscle contraction
Describe how nuke receptors work
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)
What types of molecules do nuek receptors bind and how does that effect Kd
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
GPCR pathway
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
Common nuke receptor ligands
steroid hormons like progesterone estrogen , testoesrone etcvitamin D (again hdyrophobicS
What can nuke binding to homeobod mean
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 (
Binding to DNA from nuke receptors how?
zinc fingers - some recogzinie repeating 6 bp sequences etc
How do G proteins help tune signal response time
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
How do G proteins help tune signal response time
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
Typical alpha subunit function vs Beta and gamma
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)
Neutral antagonist vs inverse agaonist vs agonist vs partial
Agonist is full rate, neutral keeps it at the same basal rate, inverse agaonist puts below basal and partial is somerate
4 steps in the G protein cycel
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
glucose to mannose
Carbon 2 switch position
Glucose to galactose
Carbon 4 swtich position
l vs d
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
glucsose to fucose
go to galactose (carbon 4 switcH) then remove OH off of methyl alcohol
glucose to xylose
get rid of methyl alcohol
glucose to ribose
get rid of 3 carbon (keep all the directionality the same)
Hhow do terpene synthases deal with reactive intermediates
active site positoned in a way H2O can’t attack - and generally for these carbocations react them with pi bonding orbitals
What amino acids stabilize in FA synth (particularly the reduction steps)
Tyrosine and Lysine
homoe vs heterodimer
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
Why did they look at human gut microbiome
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
2 enzymes they used (blood paper0
as FpGalNAc deacetylase (FpGalNAcDeAc) and FpGalactosaminidase (FpGalNase)
Know what aldol condensation looks like and how to do
Protein glycosylation vs glycoprotein
protein glyocsylation is non enzymatic but the lysine interactions with the sugar andattaches where the anomeric carbon alcohol would be
how does protein prenylation occur
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.
Amino acids relevant in other paper
N165 and N234
Know details of the moedling paper
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
