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BIOL 200 > KH5 > Flashcards

KH5 Flashcards

1
Q

what is the activity that proteins must do to preform their diverse functions

A

BINDING
they bind to each other, other macromolecules, small molecules and ions

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2
Q

what is a ligand

A

molecule that a protein binds to

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3
Q

what happens when ligand binds sometimes

A

ligand binding changes conformation of protein
ligand induced conformational change is integral to mechanism of action of many proteins

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4
Q

name the 2 important properties in ligand binding

A

specificity
affinity

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5
Q

what is specificity

A

ability of a protein to bind to only one particular ligand
even in presence of a vast excess of irrelevant molecules

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6
Q

what is affinity

A

tightness or strength of binding
expressed as dissociation constant (Kd)
stronger interaction = lower Kd
weak interaction = high Kd

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7
Q

what is protein binding

A

interaction between complementary molecular surfaces - like a puzzle piece
arises from numerous interactions - individually weak but collectively strong

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8
Q

describe a stable complex vs less stable complex in protein binding

A

stable = puzzle piece fit, grooves match up, ionic bond, hydrogen bond, hydrophobic and van der waals interactions, charges attract
less stable = more irregular fit, no consistent pattern of complementarity, charges repel and disrupts

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9
Q

describe antibody binding properties

A

bind antigens with high specificity and high affinity

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10
Q

describe how antigens and antibodies bind

A

antibodies have 2 heavy chains and 2 light chains
antigen binding surface or CDR (complementarity determining region) involves multiple protein loops from both the hc and lc
loops are highly variable in aa sequence among antibody encoding genes - many possible cdrs = many possibilities

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11
Q

what are enzymes

A

diverse class of catalytically active proteins
ligands include the substrate of the reactions they catalyze

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12
Q

where do substrate binding and reaction catalysis happen

A

at enzymes active site

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13
Q

what does substrate specificity arise from

A

substrate binding site
substrate and binding site interact at complementary molecular surfaces

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14
Q

what do aas contribute to (substrates/enzymes)

A

some contribute to substrate binding site and others to the catalytic site

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15
Q

name the 2 parameters of michaelis menten enzyme kinetics

A

Vmax and Km

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16
Q

what is Vmax

A

maximal rate of catalysis given saturating amounts of enzyme
depends on amount of enzyme and how fast it can work
it is the turnover number - enzymatic cycles per second at top speed
plateaus - when saturated

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17
Q

what is Km

A

substrate concentration that supports a rate of catalysis equal to 1/2 Vmax
depends on/is measure of affinity of enzyme substrate binding

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18
Q

how does 4 times as much enzyme affect the Vmax and Km

A

increases Vmax proportionally
Km is same tho (due to binding affinity)

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19
Q

what does binding affinity depend on

A

only the chemical properties of the enzyme and substrate
Independent of concentrations

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20
Q

name example of enzyme substrate binding and catalytic site details

A

serine protease trypsin

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21
Q

explain what happens in serine protease trypsin - what it is

A

proteases hydrolyze peptide bonds in polypeptides
serine proteases are a family of proteases whose catalytic mechanism involves a serine residue in the catalytic site

22
Q

explain what happens in serine protease trypsin - what trypsin does

A

hydrolyzes peptide bonds adjacent to arginine and lysine (large basic side chains)
proper binding occurs when substrate amino acid side chain fits into negatively charged pocket within substrate binding site

23
Q

what defines differing specificities (of substrate recognition)

A

differences in the substrate recognition pocket in related enzyme defines their differing specificities

24
Q

describe pocket in elastase

A

obstructed by bulky valine side chains - so elastase cleaves adjacent to aas with small side chains
eg - alanine and glycine

25
Q

trypsin is an example of what

A

participation of key catalytic side aa side chains in catalytic mechanism
protein folding brings distant aas into proximity
ex = trypsin - 2 step catalytic mechanism involving 3 aa side chains (not closely positioned in linear protein sequence)

26
Q

name the 3 aa side chains involved with trypsin catalytic mechanism

A

Asp-102
His-57
Ser-195

27
Q

describe first step of trypsin catalytic mechanism

A

cleavage of peptide bond with formation of covalent substrate-enzyme complex
Ser195 acyl enzyme

28
Q

describe second step of trypsin catalytic mechanism

A

hydrolysis of acyl enzyme complex (ester bond between substrate and enzyme)

29
Q

what do both sub- reactions depend on of trypsin catalytic mechanism

A

His-57’s ability to bind and to release proton
reactions best happen at a pH near the pK of His ~ pH 7

30
Q

what do enzymes exhibit

A

pH optima

31
Q

what can pH optima of enzymes reflect

A

active site acid base chemistry
sensitivity of overall protein conformation to charge distribution

32
Q

describe chymotrypsin - what it depends on…

A

depends on acid base reaction between 2 key active side residues

33
Q

what happens to chymotrypsin reaction below pH 7

A

reaction cannot occur
chymotrypsin has little activity below pH 7

34
Q

describe other proteolytic enzymes (lysosomal hdyrolases) - pH changes

A

evolved different catalytic mechanism - so they can be active in milieu of lysosomes which has low pH

35
Q

describe chymotrypsin above pH 9

A

conformation of chymotrypsin disrupted because structurally important amino groups become unprotonated and uncharged
so it has little activity

36
Q

what happens to enzymes in a common pathway

A

often physically associated with one another - either by direct binding interactions or by binding to a common scaffold protein

37
Q

what can evolution do to different enzymes

A

combine them into a single polypeptide - a multifunctional enzyme

38
Q

name an example of a multifunctional protein

A

mammalian fatty acid synthase polypeptide contains 7 different active sites catalyzing sequential steps in fatty acid synthesis

39
Q

what are allosteric effects

A

binding of ligand at one site on a protein can lead to conformational changes that affect the binding of another ligand molecule at a different site

40
Q

where are allosteric effects used majorly

A

conformational switches in regulatory proteins in response to ligand binding or post translational modification

41
Q

explain an example of allosteric effects

A

nature of the ligand bound to the nucleotide binding domain of the molecular chaperon - Hsp70
ATP vs ADP (atp = open conformation, but if hydrolyzed to adp shape changes and its a diff interaction), affects the conformation of the substrate binding domain - which changes its interactions with the misfolded client protein

42
Q

what is used as allosteric switches to control protein activity

A

noncovalent binding of Ca++ and GTP (important in cellular signal transduction pathways)

43
Q

describe Ca++ binding to calmodulin (allosteric effects)

A

changes its conformation
allows it to bind to target peptides on other proteins - thus regulating their structure and activity
turns on - makes surface where calmodulin can bind to target peptide

44
Q

describe GTP activity (allosteric effects)

A

when G proteins are bound to GTP = on conformation
when G proteins are GDP bound = off conformation
interact slightly differently with other proteins

45
Q

describe how G proteins switch from on to off (GTP activity- allosteric effects)

A

switching from on to off - facilitated by GAPs
switching from off to on - facilitated by GEFs

46
Q

what is GEF (allosteric effects) + function

A

guanine nucleotide exchange factor
must drop GDP - reaction stimulated by GEF and helps system turn on again

47
Q

what is GAP (allosteric effects) + function

A

GTPase activating protein
binds G protein and stimulates hydrolysis of GDP to help turn system off

48
Q

describe how modification of protein conformation and activity can be done

A

through phosphorylation and dephosphorylation

49
Q

what is a post translation modification

A

phosphorylation of amino acid side chains
a rapidly reversible covalent modification of protein structure

50
Q

when is phosphorylation and dephosphorylation used

A

very important for regulatory mechanisms
used in cellular transduction pathways
ex = human genome codes for over 500 different protein kinases - many are specific for just one or a few specific target proteins

51
Q

describe process of phosphorylation and dephosphorylation

A

target protein with OH can be phosphorylated (comes from ATP)
inactive state = not phosphorylated
active state = now can do something that it couldn’t before, able and ready to work, has impact on shape of protein
*change in conformations between inactive and active states

52
Q

describe cascade effect (reversible protein phosphorylation)

A

often the target of a kinase or a phosphatase is another kinase or phosphatase (just keeps attacking and amplifying each time
creates cascade effect
kinase cascade permits amplification of signs, and many levels of fine tuning

BIOL 200 (29 decks)

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