Ch.26 Flashcards
monomers
lec 26 slide 3
the building blocks
atoms or small molecules that bond together to form more complex structures such as polymers
polymers
lec 26 slide 3
a large molecule consisting of repeating units
there can be linear and branched polymers
what is radical polymerization
lec 26 slide 3
hr reacts which causes the loss of the double bond
amino acids
lec 26 slide 3
the monomers if proteins
draw a zwitterion
lec 26 slide 3
draw the general structure of an amino acid
lec 26 slide 3
what is the pka of a protonated amine
10
what is the pka of the COOH group
4-5
when is the zwitterion least soluble
at its isoelectric point
are all amino acids chiral
no, glycine isn’t due to H instead of R group
all of the other amino acids have at least one chiral carbon
what is the physiological pH
7.36
what is the equilibrium equation
HA + H2O = H3O+ + A-
based on the equilibrium equation, what does pKa equal
pKa = pH
HA = A-
in basic conditions what is the net charge of an amino acid
-1
in acidic conditions what is the net charge of an amino acid
+1
in neutral conditions what is the net charge of an amino acid
0
what is the formula for the isoelectric point
(pKa1 + pKa2) / 2
is COOH or +NH3 more water soluble when deprotonated
COOH
what nitrogen is protonated for histadine
the nitrogen attached to the double bond
how do you calculate the isoelectric point with charged side change
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)
which enantiomer is preferred for amino acids
the L enantiomer is preferred over the D
which AA is achiral
glycine
describe aliphatic amino acids
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
show how aliphatic AAs are hydrophobic
slide 9
- see diagram
- exclude water in interior of protein to generate the hydrophobic pocket
- LDFs exclude water
describe AAs with hydroxy group
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)
why are hydroxy containing AAs involved in catalysis
slide 10
- because H-bond mitigates the negative charge that would generate if attached by a nucleophile
describe sulfur containing AAs
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)
why are disulfide bonds important
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
what type of catalysis do acidic AAs engage in
slide 11
basic catalysis
what type of catalysis do basic AAs engage in
slide 12
acidic catalysis
draw basic vs. acidic catalysis
slides 11 and 12
what effects the strength of basicity of AAs
slide 12
their stability. ex. arginine is the strongest base because it can stabilize (compared to histidine and lysine
what are the uses of amide-based amino acids and draw the structure
slide 12
- increases the polarity of the compound
describe benzene rings in terms of AAs
slide 13
- aromatic side chains are useful for hydrophobic pockets
- pi stacking interactions (especially in active site)
describe pi stacking
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
what does proton transfers indicate
slide 13
acid-base reactions
describe HVK reaction
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
how do you reduce AAs
slide 16
- reactants: 1. NH3, trace acid 2. H2, Pd/C
- no stereochemical control
describe the strecker synthesis
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
do practice problem on slide 18
draw the process of an amide forming a peptide bond
slide 18
describe how the active site is stabilized
slide 19
hydrogens bonds stabilize the active state
answer slide 20
peptide vs protein
peptide is a smaller linkage of amino acids
longer polymers are referred to as proteins
where does restricted rotation occur in an amino acid and why
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.
what does an enzyme do to delta g double dagger
an enzyme catalyses a reaction which lowers the delta g double dagger of a reaction
what is delta g double dagger
the energy difference between reactants and the transition state
how does double bond character effect peaks
slide 21
- 2 peaks because of rigid double bond character (only at certain temperatures)
draw why restrictive rotation occurs between a peptide bond
slide 21
primary protein structure
slide 26
- the order of amino acid residues
- does not give any information on 3D shape
secondary protein structure
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
tertiary protein structure
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
for a tertiary protein structure, draw how a hydrogen bond holds the structure
slide 21
for a tertiary protein structure, draw how a salt bridge holds the structure
slide 29
for a tertiary protein structure, draw how hydrophobic interactions hold the structure
slide 29
for a tertiary protein structure, draw how a disulfide bond holds the structure
slide 29
describe denaturing a protein
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.
which force is sensitive to pH for protein denaturation and why
slide 36
- salt bridges are sensitive to pH because it is a bond between a positive and a negatively charged R group
is -OH sensitive to pH change
slide 36
- not really, because -OH has a high pka (~15-16), so not much dependence
is pi stacking sensitive to pH changes
slide 36
- pi stacking occurs in hydrophobic pocket which excludes water. So they are not pH dependent.
