Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Chem Bio > Chembio3 > Flashcards

Chembio3 Flashcards

You may prefer our related Brainscape-certified flashcards:
Periodic Table flashcards Chemistry 101 flashcards AP® Chemistry flashcards Biology 101 flashcards Organic Chemistry 101 flashcards
1
Q

What are 4 ways carbohdyrate building blocks can vary

A

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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What can these variations on carbohydrates do for the various carbs

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

pyranose vs furanose

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are some common conformations and what dictates them

A

chair confo - and steris orbital overlap etc

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

homo vs heteropolysaccharide

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Whats a common player (carb) in the ECM

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Proteo glycan vs glycoprotein

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is a glycosaminoglycan

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are common ways proteins and carbs are linked in glycoproteins

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How are glycolipids formed

A

covalently bonded to O

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What roles do oligosaccharides play in reecognition?

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Processive vs non processive synthesis

A

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 well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How are sugars linked together

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Describe glyocprotein synthesis

A

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 well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How are carbs added to glycoproteins

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Primary vs secondary metabolism

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How are FA’s transferred to synthesis

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

poplyketide vs prenoid subunit

A

2 vs 5 know how to draw

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Why is claisen of thioesters more favorable than that of esters

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Type I vs Type II FA synthesis

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

integral vs peripheral membane protein

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How can you predict membrane protein sequence

A

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

23
Q

How does phospholipase signalling work?

A

hydrolysis - cleaage of head groups etc

24
Q

Thioesterase uses which amino acids to cleave FA from ACp

A

Serine aspartic acidand his

25
Q

sphingo vs phosphoplipid

A

the N ont eh first FA

26
Q

Why do we care about Kd with enzyme binding

A

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)

27
Q

Fast vs slow receptros

A

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

28
Q

Describe how nuke receptors work

A

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)

29
Q

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

A

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

30
Q

GPCR pathway

A

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

31
Q

Common nuke receptor ligands

A

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

32
Q

What can nuke binding to homeobod mean

A

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 (

33
Q

Binding to DNA from nuke receptors how?

A

zinc fingers - some recogzinie repeating 6 bp sequences etc

34
Q

How do G proteins help tune signal response time

A

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

35
Q

How do G proteins help tune signal response time

A

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

36
Q

Typical alpha subunit function vs Beta and gamma

A

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)

37
Q

Neutral antagonist vs inverse agaonist vs agonist vs partial

A

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

38
Q

4 steps in the G protein cycel

A

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

39
Q

glucose to mannose

A

Carbon 2 switch position

40
Q

Glucose to galactose

A

Carbon 4 swtich position

41
Q

l vs d

A

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

42
Q

glucsose to fucose

A

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

43
Q

glucose to xylose

A

get rid of methyl alcohol

44
Q

glucose to ribose

A

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

45
Q

Hhow do terpene synthases deal with reactive intermediates

A

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

46
Q

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

A

Tyrosine and Lysine

47
Q

homoe vs heterodimer

A

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

48
Q

Why did they look at human gut microbiome

A

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

49
Q

2 enzymes they used (blood paper0

A

as FpGalNAc deacetylase (FpGalNAcDeAc) and FpGalactosaminidase (FpGalNase)

50
Q

Know what aldol condensation looks like and how to do

A
51
Q

Protein glycosylation vs glycoprotein

A

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

52
Q

how does protein prenylation occur

A

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.

53
Q

Amino acids relevant in other paper

A

N165 and N234

54
Q

Know details of the moedling paper

A

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

Chem Bio (17 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions