1A. Structure and function of proteins and their constituent amino acids Flashcards
Most AAs are in what configuration and what enantiomer is that?
S; L
Which aa has an R configuration as an L enantiomer? WHY?
Cysteine; has an SH group that has higher priority than -COOH
Which AAs are great for phosphorylation?
Threonine, Serine, and Tyrosine
Why are T, S, and Y great for phosphorylation?
They have an -OH group!
Which aa is not chiral (its alpha carbon is not chiral) and WHY?
Glycine (Only 3 different groups due to having H as its R group)
What four components make up an aa? (not counting the alpha carbon)
Amino, Carboxyl, R, H
D enantiomers have what configuration? (HINT: clockwise)
R
L enantiomers have what configuration? (HINT: counterclockwise)
S
T/F we use D enantiomers to make proteins
False; we use L enantiomers (all in S configuration except for cysteine)
which group of an aa is protonated in a typical cell (pH about 7)? Explain in terms of pH and pka.
amino (-NH3+)
pH<pka
which group of an aa is deprotonated in a typical cell? Explain in terms of pH and pka.
carboxyl (-COO-)
pH>pka
what are zwitterions? what aa category or categories may fit under this term in a typical cell (pH=7)?
molecules with net neutral charge; polar uncharged and non-polar AAs
which aa is not optically active and why
glycine; achiral
pka>pH. Protonated or deprotonated?
Protonated
pka<pH. Protonated or deprotonated?
Deprotonated
if in a high pH environment, are most aa R groups - or +?
negative; high pH means most pkas will be less than the pH
if in a low pH environment, are most aa R groups - or +?
positive; low pH means most pkas will be more than the pH
Which basic aa is actually neutral at physiological pH and why
histidine; becomes deprotonated from NH3+ since its pka is less than pH
T/F Hydrophobic AAs are found in the cytosol or exterior surface of cells
False; Hydrophobic AAs are within cell membranes because they HATE water
what does aliphatic mean
compound with Cs and Hs
All aromatic compounds are non-polar except which two and what are they categorized as?
Histidine= basic
Tyrosine= polar, uncharged
Which AAs will never be found in alpha helix secondary structures and WHY
Proline and Glycine (THINK PG)
They destabilize and break them!
what two AAs create the phosphomimetic effect? WHY? (What even is this effect?)
Glutamic (E) and aspartic (D) acid
When R groups mimic phosphate groups. Phosphate groups are negatively charged and so are E + D, which is why they mimic them! This can cause permanent activation of an aa.
what aa creates disulfide bonds
Cysteine, it has -SH (thiol or sulfhydril)
What AAs can create salt bridges? Why are these important to form?
+ and - charged AAs; help stabilize proteins!
what are two ways to make alpha amino acids?
strecker and gabriel synthesis
T/F Strecker and gabriel synthesis both form racemic mixtures
what are racemic mixtures?
True; mixture with D and L enantiomers
ammonia, aldehyde, imine, CN, aminonitrile, HCl, and H2O are all found in which reaction?
Strecker synthesis
phthalimide salt, diethyl bromomalonate, anion, R-Br, NaOH, heat, H2O, H3O+ are all found in which reaction?
Gabriel synthesis
T/F gabriel synthesis has acid catalyzed hydrolysis.
False; it has base catalyzed hydrolysis using NaOH and heat
What type of amines does gabriel synthesis make? (HINT: found in all AAs)
primary
Disulfide bonds form under oxidation conditions which is high or low ph?
High pH; less H+, will lose electrons via H
SH + SH –>SS
Disulfide bonds break under low pH. Is this oxidation or reduction conditions?
Reduction
OiL RiG
Gaining electrons via H
SS–> SH +SH
Why is BME (beta-mercaptoethanol used in Western Blot)
to break disulfide bonds
How does a peptide bond form? what does it result in?
Nucleophilic attack
Amino attacks Carboxyl to release H2O, which means it is a condensation reaction.
Results in an amide.
what type of reaction is peptide bond formation? (two types)
condensation and endergonic
endergonic vs exergonic? which is peptide bond formation and cleavage of peptide bond?
endergonic= requires E
Exergonic= releases E
Endergonic is formation. Exergonic is cleavage.
T/F Exergonic reactions are spontaneous reactions
Yes because they do not need to wait to get E since they release energy
what is hydrolysis
addition of water to cleave a molecule
why does peptide bond hydrolysis occur very slowly? also what occurs in this process?
peptide is cleaved; high Ea and resonance (stability)
what aa creates kinks in secondary protein structures due to its rigidity?
proline; also affects tertiary since it affects folding
T/F all proteins have a quaternary structure
False! All proteins must have primary, secondary, and tertiary but not quaternary
Which protein structure is linear? How is it read?
Primary; N-terminus to C-terminus by number!
What protein structure has alpha helices and beta sheets?
Secondary
Explain what beta turns are and in what structure you would find them
Loops in the peptide chain that create beta sheets in the secondary protein structure
Which are more stable and why? Parallel or Anti parallel beta sheets.
Anti parallel because the bonds are straight, short, and strong.
Parallel are at an angle, long, and weaker.
Why are alpha helices important in secondary structure of proteins?
Contain DNA binding sequences and transmembrane sequences to anchor down proteins to the membrane!
i+4 bonding sequence is seen in what protein structure? Be specific.
Alpha helices of secondary structure
What is the primary stabilizing force in secondary structure of proteins
Hydrogen bonding between O of carboxyl and H of amino
What is the term for the energetically favored folding state for a tertiary protein? Why is it favored?
Native state; maximizes entropy and minimizes intrinsic Energy
