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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

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