Chapter 4Chapter 4

Amino AcidsAmino Acids

Amino acidsAmino acids-20 common amino acids there are others -20 common amino acids there are others

found naturally but much less frequentlyfound naturally but much less frequently

Common structure for amino acidCommon structure for amino acid

COOH, -NHCOOH, -NH22, H and R functional groups all , H and R functional groups all attached to the alpha carbonattached to the alpha carbon

Ionization of amino Ionization of amino acidsacids

Three possible forms (not counting R Three possible forms (not counting R group) depending on pHgroup) depending on pH

Amino AcidsAmino Acids

Common amino acids are known as Common amino acids are known as alpha-amino acidsalpha-amino acids

Primary –NH2 replaces a H in the Primary –NH2 replaces a H in the alpha carbon atomalpha carbon atom

Soul exception – prolineSoul exception – prolinehas secondary amino group (-NH-)has secondary amino group (-NH-)

Amino acids readily ionize and are Amino acids readily ionize and are dipolar ionsdipolar ions

2

Amino Acid BasicsAmino Acid BasicspKa of the amino and carboxy differ based on R group and pKa of the amino and carboxy differ based on R group and

microenvironment. See table 4-1 pp 80 (2microenvironment. See table 4-1 pp 80 (2ndnd ed) ed) pp 76-7 pp 76-7 (3rd ed).(3rd ed). – The average is about 2.1 for the alpha carboxyl and 9.7 The average is about 2.1 for the alpha carboxyl and 9.7

for the alpha amino groups for the alpha amino groups

- Amino acids are zwitterions - a molecule with both a pos Amino acids are zwitterions - a molecule with both a pos and neg chargeand neg charge

- All naturally occurring amino acids are optically active All naturally occurring amino acids are optically active isomers, isomers, except glycineexcept glycine. .

- R-groups determine the functionality of the amino acids.R-groups determine the functionality of the amino acids.

All amino acids can be based on one of three basic groups, All amino acids can be based on one of three basic groups, non-polar, uncharged polar and charged polar (table 4-1).non-polar, uncharged polar and charged polar (table 4-1).

Also are classified based on hydrophobicity, reactivity, acidic Also are classified based on hydrophobicity, reactivity, acidic and basic nature, relative size of the side groupsand basic nature, relative size of the side groups

Non-Polar Amino AcidsNon-Polar Amino AcidsGlycine, alanine, valine, leucine and isoleucineGlycine, alanine, valine, leucine and isoleucine: : Aliphatic, Aliphatic,

inert. These are very hydrophobic amino acids with inert. These are very hydrophobic amino acids with various sized side groups. various sized side groups.

Valine, leucine and isoleucine Valine, leucine and isoleucine are branched chain and are branched chain and bulky and can cause steric hindrance. These amino bulky and can cause steric hindrance. These amino acids have a large effect on the structure of proteinsacids have a large effect on the structure of proteinsCOOH NH2 R-Group

Non-Polar Amino AcidsNon-Polar Amino Acids

ProlineProline is the only aa where the alpha amino group is the only aa where the alpha amino group is tied up in a ring structure. This amino acid is is tied up in a ring structure. This amino acid is only slightly hydrophobic. only slightly hydrophobic.

The ring structure decreases the flexibility of the The ring structure decreases the flexibility of the peptide backbone.peptide backbone.

COOH NH2 R-Group

Phenylalanine, tyrosine and Phenylalanine, tyrosine and tryptophantryptophan All are aromatic All are aromatic rings. Pi bonds / e- clouds rings. Pi bonds / e- clouds create a very hydrophobic aa. create a very hydrophobic aa. Phenylalanine is very low in Phenylalanine is very low in relative concentrations. relative concentrations.

Trp and Tyr absorb at 280 nm. Trp and Tyr absorb at 280 nm. Peptide backbone absorb at Peptide backbone absorb at 260 nm.260 nm.

Tyrosine is very reactive and is Tyrosine is very reactive and is often phosphorylated at the often phosphorylated at the OH.OH.

These aas contain phenyl and These aas contain phenyl and indol rings.indol rings.

COOH NH2 R-Group

Hydrophobic amino acids contain Hydrophobic amino acids contain sulfur. The cysteine is very sulfur. The cysteine is very reactive and involved in the reactive and involved in the structure of the protein.structure of the protein.

Involved in disulfide bonds when Involved in disulfide bonds when oxidized.oxidized.

COOH NH2 R-GroupMethionine and CysteineMethionine and Cysteine

Asparate, glutamate asparagine and Asparate, glutamate asparagine and glutamineglutamine

. . All are acidic, hydrophilic and the side groups All are acidic, hydrophilic and the side groups are involved in H bonding.are involved in H bonding.

COOH NH2 R-Group

Lysine, arginine and histadineLysine, arginine and histadineThese are basic Hydrophilic amino acids. These are basic Hydrophilic amino acids. Both the guanidino group of arginine and the imidazole ring Both the guanidino group of arginine and the imidazole ring

of histadine contain resonance forms.of histadine contain resonance forms. The histadine is the only amino acid with a side group pKa in The histadine is the only amino acid with a side group pKa in

the physiological pH range. It is often found in sites of the physiological pH range. It is often found in sites of catalysis (very reactive). catalysis (very reactive). His also is a good chelator of His also is a good chelator of divalent transition metals Zndivalent transition metals Zn+2 +2 andand NINI+2 +2 ..

COOH NH2 R-Group

Serine and threonineSerine and threonine- Only slightly hydrophilic. Only slightly hydrophilic. - The OH is only ionizable under very basic conditions.The OH is only ionizable under very basic conditions. - The OH groups are very reactive and are phosphorylated The OH groups are very reactive and are phosphorylated

similar to similar to tyrosinetyrosine.. COOH NH2 R-Group

Less Common Amino AcidsLess Common Amino Acids

Here are some amino acids that are found in proteins, but are comparatively rare.

They are not synthesized by ribosomal processes; most typically arise from post-translational modifications to the protein, which are catalyzed by specific enzymes.

Common post-translational modifications include hydroxylation, methylation, acetylation, and phosphorylation.

You are not responsible for knowing these amino acids, however, if asked you should be able to recognize that they are not one of the common 20.

More More titrationstitrations

When the amino When the amino acid is has a 0 acid is has a 0 net charge that is net charge that is considered the considered the isoelectric pointisoelectric point.. For amino acids For amino acids with side groups with side groups that contain an that contain an ionizable moiety ionizable moiety it is the average it is the average of the two pKa of the two pKa that are charged that are charged when the net when the net charge is zero.charge is zero.

Isoelectric PointsIsoelectric PointsIf the side group is not ionizable, then the pI is the If the side group is not ionizable, then the pI is the

average of the C and N groups pKaaverage of the C and N groups pKaCalculations of pI for a compound with more than Calculations of pI for a compound with more than

two dissociable groups carries more possibility two dissociable groups carries more possibility for errorfor error

First write out all possible ionic structures for a First write out all possible ionic structures for a compound in order that they occur starting with compound in order that they occur starting with the most basic to the most acidicthe most basic to the most acidic

Next, identify the isoionic, zwiterionic or neutral Next, identify the isoionic, zwiterionic or neutral representationrepresentation- The pI is the pH at the midpoint between the The pI is the pH at the midpoint between the

pK values on either side of the isoionic speciespK values on either side of the isoionic species

What about peptides or proteins?What about peptides or proteins?

The classification of the 20 amino The classification of the 20 amino acids is based on the side chainsacids is based on the side chains..

- You should know for each of the amino acidsYou should know for each of the amino acids

--The name and 3 letter designationThe name and 3 letter designation- Based on the side chain (R group) if the amino - Based on the side chain (R group) if the amino

acid is aliphatic, aromatic, sulfur containing, acid is aliphatic, aromatic, sulfur containing, hydroxyl, basic, acidic, or an amide derivativehydroxyl, basic, acidic, or an amide derivative

-The charge at high neutral and low pH-The charge at high neutral and low pH- chemical reactivity- chemical reactivity- if the amino acid is hydrophobic or - if the amino acid is hydrophobic or

hydrophilic, acidic or basic, polar, uncharged hydrophilic, acidic or basic, polar, uncharged but polar and charged polar.but polar and charged polar.

- relative size- relative size

Peptides & Primary StructureProtein FunctionsProtein Functions

– Enzymes -Catalyze a thermodynamically favorable Enzymes -Catalyze a thermodynamically favorable reactionreaction

– Storage/transport - binding proteins fatty acids w/albuminStorage/transport - binding proteins fatty acids w/albumin– no catalytic activity but do form chemical bonds with no catalytic activity but do form chemical bonds with

ligandsligands– Structure - Several levelsStructure - Several levels– cytoskeleton, collagen, bone ...cytoskeleton, collagen, bone ...– ReceptorsReceptors– Growth factorsGrowth factors

Amino Acid / protein modificationAmino Acid / protein modification Acetylation -Acetylation - Hydroxylation - Hydroxylation - Phosphorylation - Phosphorylation - Carboxylation - Carboxylation - lipid esterification -lipid esterification -

The formation of a The formation of a peptide bond peptide bond occurs by the loss occurs by the loss of a water or of a water or dehydration of dehydration of water from the a water from the a carboxyl and of one carboxyl and of one amino acid and the amino acid and the a amino of another a amino of another amino acidamino acid

PeptidesPeptidesWhen amino acids are linked together it is When amino acids are linked together it is

through the formation of a peptide bondthrough the formation of a peptide bond

Each amino acid is called a residueEach amino acid is called a residue

Addition of acid or base hydrolyzes the peptide bond and adds Addition of acid or base hydrolyzes the peptide bond and adds water back across the peptide bond.water back across the peptide bond.

The amino (N) terminal is written on the left and the carboxyl (C) The amino (N) terminal is written on the left and the carboxyl (C) terminal is on the right.terminal is on the right.

The actual sequence of amino acids is considered the primary The actual sequence of amino acids is considered the primary structure. No other factor is considered in this level of structure. No other factor is considered in this level of structure. Most DNA mutations have there effect at the primary structure. Most DNA mutations have there effect at the primary level.level.

++HH33NNCCHH

CC

OO

NNHH

RR

CCHH

RR

CC

OO

NNHHCCHH

CCOOOO--

RR

++HH33NNCCHH

CC

OO

NNHH

RR

CCHH

RR

CC

OO

NNHHCCHH

CCOOOO--

RR

Peptide bondPeptide bond– Rx of bond formation costs energy (ATP) but Rx of bond formation costs energy (ATP) but

degradation of proteins is thermodynamically degradation of proteins is thermodynamically favorable. (entropy)favorable. (entropy)

– C-N bond shorter than normal and more like double C-N bond shorter than normal and more like double bondbond

– This results in rigid planar, non-rotating links This results in rigid planar, non-rotating links between aabetween aa

– Size of peptides and proteins are described in Size of peptides and proteins are described in DaltonsDaltons

– 1 atomic unit = 1 dalton ; MW = Dalton / kd;1 atomic unit = 1 dalton ; MW = Dalton / kd; Mr=molecular weightMr=molecular weight

Many peptides have Many peptides have important biological important biological

activitiesactivitiesBiologically important Biologically important

peptidespeptides

Insulin - Insulin - – Short peptide produced Short peptide produced

as a pre-pro-peptide. as a pre-pro-peptide. The initial peptide is The initial peptide is much longer and is much longer and is modified twice, each modified twice, each time a set of peptide time a set of peptide bonds are hydrolyzed. bonds are hydrolyzed. The final shortened The final shortened version is active. There version is active. There are two subunits, held are two subunits, held together by a disulfide together by a disulfide bond.bond.

Oxytocin and VasopressinOxytocin and Vasopressin– Start as long precursors in hypothalamus- whose Start as long precursors in hypothalamus- whose

final form is 9 aafinal form is 9 aa– differ by 2 residuesdiffer by 2 residues

oxytocin - uterine contraction during childbirth and oxytocin - uterine contraction during childbirth and milk production during lactationmilk production during lactation

vasopressin - alters blood pressure by forcing kidney to vasopressin - alters blood pressure by forcing kidney to retain water, increasing the volume of bloodretain water, increasing the volume of blood

Met-enkephalin (opioid peptides)Met-enkephalin (opioid peptides)» Naturally produced peptides, bind to receptors, Naturally produced peptides, bind to receptors,

and reduce pain cause pleasure. Morphine likeand reduce pain cause pleasure. Morphine like

Substance PSubstance P » Opposite effect from opioids Opposite effect from opioids » Stimulates perception of pain (protective Stimulates perception of pain (protective

mechanism)mechanism)