119 terms

Kaplan MCAT OChem 15: Amino Acids, Peptides, and Proteins

these groups attached to alpha carbon

amine group

carboxyl group

alpha -H

R-group (variable side chain)
alpha carbon is a chiral (stereogenic) center
all of these are optically active
AA naturally occurring
are all L enantiomers, w/ amino group on the left
have S config, except for cysteine, since sulfur priority /
simplest AA, isn't chiral at alpha carbon
AA has both a basic amino group and an acidic carboxyl group
play either role depending on the conditions
amphoteric amino group as base
lots of protons in solution => amino acid will pick up a proton in AA
acid-base characteristics amino group as acid
amino group donates proton in AA
amino group positive when protonated and carboxyl group take neg charge when deprotonated => both charges same time form this dipolar ion => neutralize each other => neutral pH => in form of internal salts
acid base character of AA - Ka1, Ka2, Kb1, Kb2
since there are two different locations either protonated or deprotonated have at least two different dissociation constants,
neutral AA in acidic solution
becomes fully protonated

amino group easily since protonated at neutral pH

takes fairly acidic environment to protonate the carboxyl group
neutral AA in basic sol
AA become fully deprotonated

carboxyl group group easy to deprotonate (since this way at neutral)

takes more alkaline environment to deprotonate amino group
at low pH, AA
carries excess pos. charge
at high pH AA
carries excess neg. charge
isoelectric point (pI) or isoelectric pH
intermediate pH at which AA exists as zwitterion of AA
isoelectric point (pI) or isoelectric pH
must lie between pKa1 and pKa2
is simply the pH at which dissociation occurs.
higher Ka
lower pkA
isoelectric point (pI) or isoelectric pH
AA is uncharged
titration of AA
curve ends up looking like comobo of two or three monoprotic acids
titration of AA steps example (base added to acid)
1 M glycine is acidic, fully protonated w/ pos charge => titrated w/ NaOH => carboxyl group will be first to lose proton and amino acid acts as buffer => pH changes slowly => when 0.5 moles base added => original and zwitteron are equimolar, where pH = pKa1 => solution buffered against pH changes (buffer zone) => add more base => more carboxyl groups will become deprotonated => AA start losing buffering capacity => pH will rise quickly => 1 mole of base => full zwitterion => glycine and base equal amounts => electrically neutral, so equal isoelectric point (pI) and pH =pI => add more base through 2nd buffering stage = > amino group starts to deprotonate => 1.5 moles base => zwitterion and neg charge equimolar => pH = pKa2 => 2 moles base now => only neg charge moecule
tiration of AA rule
1. when adding base, carboxyl, then amino group, loses proton.

2. two moles of bases added to deprotonate one most of mass amino acids

3. buffer capacity of AA greatest at or near pH of two disso. pKa1 and pKa2; at isoelectric point, its buffering capacity is minimal

4. some AA has acidic or basic side chains; to find pI of these amino acids, avg the two acidic pKa's if side chain is acidic and pKa's if side chain is basic

5. possible to perform reverse
henderson-hasselbalch equation
relates the pH to the ratio of CA to CB
henderson-hasselbalch equation
when pKa1 of glycine is known. the ratio of acids to its conjugate base for a particular pH
henderson-hasselbalch equation
can prepare effective buffer solution of AA

best buffering regions of AA occur w/in one pH unit of pKa or pKb
types of amino acids
nonpolar, polar, acidic, basic
nonpolar AA
most have R groups that are saturated hydrocarbons, meaning hydrophobic and dec. solubility of AA in water
nonpolar AA
prefer to be buried inside proteins, away from aq. cell environment
nonpolar AA (trypotophan)
has a N w/ lone pair => resonate through aromatic ring => doesn't exist basic properties

large and hydrophobic, often nucleating residue when proteins fold
polar AA
uncharged polar R groups that are hydrophilic; inc solubility in water

often on surface of proteins
types of AA found in regions of proteins exposed to aq. polar environment
polar, acidic, basic
acidic AA
R group has carboxyl group, neg charge at 7.4 => salt form in body
acidic AA
roles in substrate binding sites of enzymes and reactions that require a proton transfer
acidic AA
end in -acid (easier to remember)
acidic AA
have three distinct pKa's
acidic AA (aspartic and glutamic acid)
each have three groups that must be neuralized during titration (two COOH and one NH3+) => three pKa1..=> isoelectric point shifted towards acidic pH (found by avg both acidic pKa's)
acidic AA (aspartic and glutamic acid)
three moles of base deprotonate each mole of acidic AA
basic AA
side chain contain amino group that will carry a pos charge

has three disso. constants
basic AA
isoelectric point shifted toward an alkaline pH (found by averg two basic pKas)
basic AA
three moles of acid neturalize one mole of basic amino acid
composed of AA subunits, sometimes called residues
peptide bond
when two AA w/ these groups combine, this is formed, which is an amide bond, forms between them
basically small proteins
peptide vs. protein
vague, but usually peptides contain fewer than 50 residues
two AA joined together
many AA linked together
peptide rxns
to form pep bond => condensation occurs (water loss)
peptide rxns
reverse rxn, hydrolysis (cleavag by adding water) of peptide bond, is catalyzed by acid or base
peptide rxns
certain enzymes digest chain at specfic peptide linkages
amino/N terminal
terminal AA w/ free alpha amino group (end on the left)
carboxy/C terminal
terminal AA w/ free carboxyl group (end on right)
two resonance structures w/ partial DB character between N and carbonyl carbon => C-N is restrited => rigidity and stability of backbone of proteins
polypeptide that range from only a few to more than a thousand amino
functions of proteins


memebrane pores


elements of cell structure.
main actors of bio systems
four levels of protein structure
primary, secondary, tertiary, and quaternary
primary structure
coded into DNA of organism
primary structure
it's the sequence of AA, listed from N-terminus to C-terminus, each linked by peptide bonds
primary structure
most fundamental structure of protein
primary structure
sequence that determines all higher levels of protein structure
primary structure
a protein will assumble 2, 3, 4th strutures most energetically favorable for given this
primary structure
can be determined in lab using sequencing
primary structure can be determined in lab using this; most easily done on DNA (gene) that produced the protein
secondary structure
local structure of neighboring AA
secondary structure
result of H bonding between nearby AA
two most common types of secondary structure
α-helix and β-sheets (or β-pleated sheet)
may be parallel or antiparallel
is a rodlike structure in which peptide chain coils clockwise about central axis
this is stabilized by intramolecular H bonds between carbonyl oxygen atoms and amide H atoms four residues away from each other (n +4 H bond)
side chains point away from helix core, interacting w/ cell environment
typical protein w/ this structure is keratin
a fibrous structural protein that's found in our hair and fingernails
β-pleated sheets
peptide chains lie alongside each other => forming rows
β-pleated sheets
chains held together by intramolecular H bonds between carbonyl O atoms on one peptide chain and amine H atom on another
β-pleated sheets
assumed rippled, or rippled, or pleated shape to accommodate greateset possible number of H bonsd
β-pleated sheets
R groups of amino residues point above and below the plane of this
β-pleated sheets
silk fibers composed of this
tertiary structure
3D shape of protein
tertiary structure
mostly determined by hydrophobic and hydrophilic interactions between R groups of amino acids
tertiary structure
also determined by dist'n of disulfide bonds
disulfide bonds (tertiary structure)
results when two cysteine molecules become oxidized to form cystine

these create loops
AA proline
due to ring shape => can't fit into every location in α-helix => causes kink in chain
two major classification of tertiary structures
fibrous and globular proteins
fibrous proteins
such as collagen, found in sheets or long strands
globular proteins
such as myoglobin, are spherical
quarternary structure
protein can have this structure ONLY if contains more than one polypeptide subunit
quarternary structure
refers to way subunits arrange themselves to yield functional protein
quarternary structure
example is hemoglobin
O transporting machines that fill our red blood cells

composed of four diff. globular protein subunits
primary structure
consist of AA sequence and covalent bonds
secondary structure
refers to the local structure of a protein as determined by H bond
tertiary structure
3D shape of protein
quaternary structure
arrangement of polypeptide subunits
conjugated proteins
type of proteins that have prosthetic groups
conjugated proteins
derives part of function from covalently attached molecules called prosthetic groups
prothestic groups (conjugated proteins)
can be organic molecules like vitamins, or even metal ions
proteins w/ lipid, carbs, and NA prosthetic groups

major roles in determining function of respective proteins
heme group
each of hemoglobin's subunits (as well as myoglobin) contain this prosthetic group
heme group
composed of an organic porphyrin ring w/ an Fe atom bound in center
heme group
itself binds to and carries O

hemoglobin would be inactive w/o this
binds oxygen cooperatively => easier to bind 2nd molecule of oxygen
denaturation/melting of proteins
proteins lose their 3D structure and revert to a random-coil state => completely functionless
methods for denaturation/melting of proteins

change in pH


solute conc
denaturation/melting of proteins
weak IMF that keep protein stable and functional can be disrupted by factors
denaturation/melting of proteins
when this happens, damage is usually permanent; however, certain gentle denaturing agents (like urea) don't permanently disrupt protein => remove reagent => might renature (so reversible)
nonpolar and polar AA in neutral solution
as zwitterions
acidic AA in neutral
neg. charge ions
basic AA in neutral
pos. ions
all AA
have at least two pKa's
is between the two pKa's in all AA
AA pI (acidic)
w/ three pKa's, this is between two largest pKa's
AA pI (basic)
w/ three pKa's, this is between two lowest pKa's
buffer zone
pH = pKa
pH = pI
all species have been deprotonated, and pH change drastically