3: Amino Acids

amino acids common structural features

- alpha carbon w/4 substituents

- alpha carbon is the chiral center

- read from N terminus to C terminus

- tetrahedral

- R group is different for each amino acid -> the characteristic

which amino acids is not chiral

Glycine -> R group is H

which amino acids are not tetrahedral?

proline

-> R group turns back on itself

most amino acids are (D/L)?

L -> bc most enzymes are L -> amino acids are recognized

all amino acids are L (S) except cystine which is R

classification of R groups

- nonpolar, aliphatic (7)

- aromatic (3)

- polar, uncharged (5)

- positively charged (3) -> histidine is partially charged

- negatively charged (2)

nonpolar, aliphatic R groups

- glycine, alanine, proline, valine, leucine, isoleucine, methionine

- hydrophobic effect stabilize protein structure

- proline -> folding -> due to hydrophobic and hydrogen bonding

small amino acids are more _______

commonly found -> easier to make

which amino acid has a -SH group?

cysteine -> can spins R

histidine pka is

R group pKa = 6 -> close the body pH -> easily protonates and deprotonates

N terminus pKa = 9 -> basic

C terminus pKa = 2 -> acidic

aromatic R groups

- phenylalanine (260nm), tyrosine (270nm), tryptophan (280nm)

- absorb UV light at 270-280nm

- can contribute to the hydrophobic effect

Polar, uncharged R groups

- serine, threonine, cysteine, asparagine, glutamine

- can form H bonds

- cysteine can form disulfide bond -> helps lock a protein in its place

positive charge R groups

- lysine, arginine, histidine

- have significant positive charge at pH 7

- arginine is found at inactive sites w/negative substrate

negatively charged R groups

- aspartate, glutamate

- net negative charge at pH 7

uncommon amino acids

- modifications of common aminos: (1) modified after protein synthesis; (2) modified during protein synthesis; (3) modified transiently to change protein's function

- free metabolites

amino acids can acts as ______

weak acids and bases

- zwitterion is at neutral pH

pI

- isoelectric point

- pH at which the net electric charge is zero

- pI = (pK1 + pK2)/2

- pH > pI -> net neg charge

- pH < pI -> neg pos charge

effect of chemical environment on pKa

- α-carboxyl group is more acidic than in carboxylic acids

- α-amino group is less basic than in amines

- so 2 buffer regions, one for α-carboxyl and other for α-amino groups

amino acids with ionizable side chains properties

- have pKa value

- act as buffers

- influence the pI of the amino acid

- can be titration -> 3 ionization steps -> α-amino, α-carboxyl, and R group (if possible)

- helps distinguish peptides

dipeptide

2 amino acids bonded together w/1 peptide bond

tripeptide

3 amino acids w/2 peptide bonds

oligopeptides

2-10 amino acids bonded

polypeptides

10-50 amino acids bonded

protein

50-100+ amino acids bonded

multisubunit proteins (aka aminomonomers)

2+ polypeptides associated noncovalently

oligomeric protein

at least 2 identical subunits

protomers

identical units

How to estimate the number of amino acid residues

- # of resides = molecular weight/110

- 110 comes from the average molecular weight of amino acids (~128) minus the water molecule removed (10)

conjugated proteins

- contain permanently associated chemical components

- prosthetic group : non-amino acid part

- lipoproteins : contain lipids

- glycoproteins : contain sugars

- metalloproteins : contain specific metals

proteins are separated based on ________

size, charge, binding properties, and solubility

how to purify proteins

1) break open tissue or cell

- crude extract : releases proteins in solution

2) fractionation : separate proteins into fractions based on size or charge; uses salt to selectively precipitate proteins

3) dialysis : use semipermeable membrane to separate proteins from small solutes

column chromatography

- uses buffered solution (mobile) to migrate through porous solid material. the buffered solution w/proteins migrates through the solid phase. the rate of migration highlights the different proteins

- can separate based off sign and magnitude of net charge, size, and binding affinity to a solution

which amino acid is not tetrahedral?

proline and its derivatives -> due to folding back to the amino group

n terminus pKa is around

9

c terminus pKa is around

2 or 4 (if bonded w/peptide bonds)

overall charge of a polypeptide is _____

the net charge of the amino acids at pH ~7.4

need to look at the R groups and if it is charged or not

what amino acids are hydrophobic?

alanine, isoleucine, leucine, phenylalanine, proline, and valine

basically the nonpolar ones

what amino acids are hydrophillic?

glycine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, histidine, serine, and threonine

notice how they are polar

what amino acids are amphipathics?

lysine, methionine, tryptophan, and tyrosine

What drives protein folding?

- hydrophobicity

- notice that hydrophobicity -> decrease entropy -> however increase H bonding potential via folding -> dH < 0 -> enthalpy driven rxn to make dG < 0

which amino acids can H bond w/h2o?

those with -OH or -S- or -SH

which amino acids are negative at pH 7?

those with COO- -> aspartate and glutamate

which amino acids are positive at pH 7?

those with NH3 + -> histidine (kinda of), lysine, and arginine

why do we use R/S instead of D/L?

R/S is used bc some amino acids have 2 chiral centers, so we can use R/S system to name the amino unambiguously

what are the essential amino acids

arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalnine, threonine, tryptophan and valine

what are the nonessential amino acids

alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine and tyrosine

what is special about tyrosine

our body just modifies phenylalanine (essential) so we dont produce tyrosine from start to finish like other nonessential amino acids

what makes an amino acid essential?

- our bodies can not make the amino -> must be obtained from diet

- this is due to large amount of synthesis steps -> usually the bigger sized ones

- since we need to get nonessential aminos from a diet they are not frequently in proteins

covalent modification

- post-translational

- convalently modifies an amino acid in a protein (aka a side chain)

- on/off switches

common covalent modifications

phosphorylation (most) , acetylation , and methylation (least)

phosphorylation

- adds -PO3 2-

- usually on S, T, Y, H

- ex hormone receptors and regulator enzymes

- kinases : removes the phosphate from the ATP and add it to the amino

- phosphatases : removes the phosphate group

- add a negative charge

Acetylation

- adds COCH3

- usually on K

- ex histones and metabolic enzymes

- uses Acetyl-CoA

- acetylases : adds the acetyl

- deacetylases : removes the acetyl

- adds a negative charge -> neutralizes positive charges -> usually lysine

methylation

- adds -CH3

- usually on K, R

- ex histones

- uses methyl donors (SAM)

- methylases : adds the methyl group

- demethylases : removes the methyl group

- does not add any charges -> no neutralization of positive charges

GFP

- green fluorescent protein

- in jellyfish

- auto-modifies the protein -> no enzymes needs

- requires oxygen

- used to tag any protein

Amino acid UV absorption

Phe < Tyr < Trp

260 < 270 < 280

- these absorption of uv light is what makes these amino acids responsible for inherent fluorescence of proteins

beer lambert's law

A = Ecl

- used to determine protein concentration