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CH 336 > Ch.26 > Flashcards

Ch.26 Flashcards

1
Q

monomers

A

lec 26 slide 3

the building blocks
atoms or small molecules that bond together to form more complex structures such as polymers

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2
Q

polymers

A

lec 26 slide 3

a large molecule consisting of repeating units
there can be linear and branched polymers

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3
Q

what is radical polymerization

A

lec 26 slide 3

hr reacts which causes the loss of the double bond

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4
Q

amino acids

A

lec 26 slide 3

the monomers if proteins

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5
Q

draw a zwitterion

A

lec 26 slide 3

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6
Q

draw the general structure of an amino acid

A

lec 26 slide 3

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7
Q

what is the pka of a protonated amine

A

10

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8
Q

what is the pka of the COOH group

A

4-5

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9
Q

when is the zwitterion least soluble

A

at its isoelectric point

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10
Q

are all amino acids chiral

A

no, glycine isn’t due to H instead of R group

all of the other amino acids have at least one chiral carbon

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11
Q

what is the physiological pH

A

7.36

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12
Q

what is the equilibrium equation

A

HA + H2O = H3O+ + A-

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13
Q

based on the equilibrium equation, what does pKa equal

A

pKa = pH
HA = A-

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14
Q

in basic conditions what is the net charge of an amino acid

A

-1

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15
Q

in acidic conditions what is the net charge of an amino acid

A

+1

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16
Q

in neutral conditions what is the net charge of an amino acid

A

0

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17
Q

what is the formula for the isoelectric point

A

(pKa1 + pKa2) / 2

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18
Q

is COOH or +NH3 more water soluble when deprotonated

A

COOH

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19
Q

what nitrogen is protonated for histadine

A

the nitrogen attached to the double bond

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20
Q

how do you calculate the isoelectric point with charged side change

A

if the side chain is acidic (COOH) –> average the pka values of the ACIDS (ex. COOH and R group)

if the side chain in basic (+NH3) –> average the pka values for the BASES (ex. +NH3 and the R group)

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21
Q

which enantiomer is preferred for amino acids

A

the L enantiomer is preferred over the D

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22
Q

which AA is achiral

A

glycine

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23
Q

describe aliphatic amino acids

A

slide 9
- have nonpolar (hydrophobic) side chains
- in proteins, they generally make up the interior and are useful for repelling water water and creating hydrophobic environments

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24
Q

show how aliphatic AAs are hydrophobic

A

slide 9
- see diagram
- exclude water in interior of protein to generate the hydrophobic pocket
- LDFs exclude water

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25
Q

describe AAs with hydroxy group

A

slide 10
- are polar protic with the side chains capable of forming H-bond networks with water
- no acid base effects on the side chain because the OH on the R group has a pKa of 15-16 (to difficult to deprotonate)

26
Q

why are hydroxy containing AAs involved in catalysis

A

slide 10
- because H-bond mitigates the negative charge that would generate if attached by a nucleophile

27
Q

describe sulfur containing AAs

A

slide 10
- used to create hydrophobic pockets in proteins
- generally found in the interior of proteins
- have redox activity (a type of chemical reaction that involves a transfer of electrons between two species)

28
Q

why are disulfide bonds important

A

slide 11
- cysteins contain a thiol group (R-S-H) which can be oxidized to disulfides. The disulfides can be reduced back to thiols
- disulfide bonds are important when considering overall protein folding

29
Q

what type of catalysis do acidic AAs engage in

A

slide 11
basic catalysis

30
Q

what type of catalysis do basic AAs engage in

A

slide 12
acidic catalysis

31
Q

draw basic vs. acidic catalysis

A

slides 11 and 12

32
Q

what effects the strength of basicity of AAs

A

slide 12
their stability. ex. arginine is the strongest base because it can stabilize (compared to histidine and lysine

33
Q

what are the uses of amide-based amino acids and draw the structure

A

slide 12
- increases the polarity of the compound

34
Q

describe benzene rings in terms of AAs

A

slide 13
- aromatic side chains are useful for hydrophobic pockets
- pi stacking interactions (especially in active site)

35
Q

describe pi stacking

A

slide 13
- occurs especially in the active site
- requires more than one aromatic group
- draw the partial positivity and partial negativity of benzene
- draw the different ways a benzene may pi stack

36
Q

what does proton transfers indicate

A

slide 13
acid-base reactions

37
Q

describe HVK reaction

A

slide 15
- synthesis of AAs
- first reactants: 1. Br2, PBr3 1. H2O
- second reactants: 1. NH3 xs 2. HA
- not enantiomerically pure (you get a racemic mixture on the NH2

38
Q

how do you reduce AAs

A

slide 16
- reactants: 1. NH3, trace acid 2. H2, Pd/C
- no stereochemical control

39
Q

describe the strecker synthesis

A

slide 17
- must start from an aldehyde
- reactants: 1. NH3, trace acid 2. HCN 3. acid, heat
- adds a carbon due to the HCN
- trick: find the alpha carbon, the side group should remain the same

40
Q

do practice problem on slide 18

A
41
Q

draw the process of an amide forming a peptide bond

A

slide 18

42
Q

describe how the active site is stabilized

A

slide 19
hydrogens bonds stabilize the active state

43
Q

answer slide 20

A
44
Q

peptide vs protein

A

peptide is a smaller linkage of amino acids
longer polymers are referred to as proteins

45
Q

where does restricted rotation occur in an amino acid and why

A

slide 21
- occurs between a carbonyl and the amide
- restricted rotation lowers the degree of freedom of the system
- occurs because of their partial double bond character. This is due to the delocalization of electrons from the double-bonded oxygen to the peptide bond.

46
Q

what does an enzyme do to delta g double dagger

A

an enzyme catalyses a reaction which lowers the delta g double dagger of a reaction

47
Q

what is delta g double dagger

A

the energy difference between reactants and the transition state

48
Q

how does double bond character effect peaks

A

slide 21
- 2 peaks because of rigid double bond character (only at certain temperatures)

49
Q

draw why restrictive rotation occurs between a peptide bond

A

slide 21

50
Q

primary protein structure

A

slide 26
- the order of amino acid residues
- does not give any information on 3D shape

51
Q

secondary protein structure

A

slide 27
- protein chains interact with themselves via hydrogen bonding in the backbone
- they primarily form two secondary structures: alpha helix and beta pleated sheets

alpha helix = coiled loop; a protein containing alpha helices is flexible and stretchy; H bonding occurs between NH (first) and C=O (second)
beta pleated sheet = H-bonds between strands in the backbone that sit side by side; they are strong but not flexible

52
Q

tertiary protein structure

A

slide 29
- defines how a protein “folds” to achieve its active form (its overall 3D shape)
- held together by side chain interactions including H-bonding, salt bridges, hydrophobic effects, disulfide bonds, and pi-stacking

53
Q

for a tertiary protein structure, draw how a hydrogen bond holds the structure

A

slide 21

54
Q

for a tertiary protein structure, draw how a salt bridge holds the structure

A

slide 29

55
Q

for a tertiary protein structure, draw how hydrophobic interactions hold the structure

A

slide 29

56
Q

for a tertiary protein structure, draw how a disulfide bond holds the structure

A

slide 29

57
Q

describe denaturing a protein

A

slide 33/35
- structure is critical to the proteins function
- many of these features are held together by very specific chemical interactions
- disrupting these interactions leads to a protein being denatured (prevents the protein from working any longer)
- IM forces are fairly weak. Heat and agitation disrupt. They can then rearrange which denatures the protein.

58
Q

which force is sensitive to pH for protein denaturation and why

A

slide 36
- salt bridges are sensitive to pH because it is a bond between a positive and a negatively charged R group

59
Q

is -OH sensitive to pH change

A

slide 36
- not really, because -OH has a high pka (~15-16), so not much dependence

60
Q

is pi stacking sensitive to pH changes

A

slide 36
- pi stacking occurs in hydrophobic pocket which excludes water. So they are not pH dependent.

CH 336 (6 decks)

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