A Ala Alanine Alanine is a small, hydrophobic residue. Its side chain, R, is just a methyl group. Alanine likes to sit in an alpha helix, it doesn’t like beta strands very much, but it hates beta- turns. If you want to mutate a residue, but you don’t have a good plan about what to replace it with, take alanine because it is a subset of all other amino acids ©CMBI 2001

C Cys Cysteine Cysteine is a small hydrophobic residue. It doesn’t like the alpha helix, but doesn’t mind strands. It can form bridges with other cysteines (Cys-Cys bridges). It can bind metals (especially Zn and Cu). The S-H group is very reactive and can easily be oxidised. ©CMBI 2001

D Asp Aspartic acid Aspartic acid, or aspartate, is an intermediately large, hydrophilic, negatively charged residue. Its side chain normally titrates at pH 4.5. It likes to sit near the N- terminus of a helix, and in turns. It hates strands. It often occurs in active sites. It can bind ions (mainly Ca). ©CMBI 2001

E Glu Glutamic acid Glutamic acid, or glutamate, is a large, hydrophilic, negatively charged residue. Its side chain titrates at pH 4.6. It loves the helix, doesn’t mind being in a strand, but is not so good for turns. ©CMBI 2001

F Phe Phenylalanine Phenylalanine is a large, hydrophobic, aromatic residue. It is good for a strand, it doesn’t mind sitting in a helix, but it hates the turn. ©CMBI 2001

G Gly Glycine Glycine is the smallest residue. It doesn’t have a side chain, so its hydrophobicity is a bit undetermined. The fact that it doesn’t have a side chain means that its backbone is very flexible so that it can make backbone turns that other residues cannot make. It is very bad for helix, bad for strand, but it is the star of the turns. ©CMBI 2001

H His Histidine Histidine is very special. It is a large hydrophilic residue. Both its side chain nitrogens can titrate (the first one at pH 6.2). It is a little bit aromatic. It is not particularly picky about its secondary structure. It is often seen in active sites. It is neutral at physiological pH, but it can easily become positive, and occasionally even negative. It can bind metal ions (mainly Zn, Ni, Cu). ©CMBI 2001

I Ile Isoleucine Isoleucine is an intermediately large, hydrophobic residue. It is beta branched which means that it likes to sit in a strand. It doesn’t mind sitting in a helix either, but it cries its eyes out in a turn. ©CMBI 2001

K Lys Lysine Lysine is a large, hydrophilic, positively charged residue. It is not a good strand residue, but it doesn’t mind sitting in a helix or in a turn. Its side chain is very long and flexible. ©CMBI 2001

L Leu Leucine Leucine is an intermediately large, hydrophobic residue. It really loves to sit in a helix. It is also good for a strand, but it hates turns. ©CMBI 2001

L Leu Leucine LEUCINE IS THE MOST ABUNDANT AMINO ACID IN PROTEINS IN MEMBRANE PROTEINS THE AMOUNT OF LEU IS EVEN HIGHER.

L Leu Leucine LEUCINE IS CONSIDERED THE "SWITCH" THAT STIMULATES PROTEIN SYNTHESIS. THE COMBINATION OF WHEY PROTEIN AND ADDED LEUCINE MAXIMIZES MUSCLE PROTEIN SYNTHESIS BEFORE AND AFTER RESISTANCE EXERCISE.

M Met Methionine Methionine is a large, sulphur containing, hydrophobic residue. It loves helices, doesn’t mind sitting in a strand, but it hates turns. Methionine can bind metals with its sulphur, but this sulphur is not reactive. It is often the first residue of a molecule. The N-terminus is mostly positive and thus mostly at the surface. However, very often the N- terminal Methionine is not present in mature proteins. ©CMBI 2001

M Met Methionine Methionine is THE Methyl donor in biological processes: S-Adenosyl methionine (SAM) Methylation is an increasingly interesting topic especially in relationship to DNA methylation: epigenetics. However, also during ageing methylation pattern changes -  environmental factors.

Age can be calculated from methylation

Michele Zampieri, Fabio Ciccarone, Roberta Calabrese, Claudio Franceschi, Alexander Bürkle, Paola Caiafa Mechanisms of Ageing and Development, 2015, Available online 20 February 2015 Demethylation can occur via TET enzymes

RC Grandison et al. Nature 000, 1-4 (2009) doi: /nature08619 Methionine is necessary and sufficient to increase dietary restriction fecundity.

N Asn Asparagine Asparagine is an intermediately large, polar residue. It hates the helix, is mildly un- amused in a strand, but it loves the turn. It can bind metal ions (Ca), but doesn’t do that as well as its isosteric partner aspartic acid. ©CMBI 2001

P Pro Proline Proline is small and hydrophobic. In proline, the side chain is connected to the backbone at two places: the C  and the N. Proline does not have a backbone proton*, and thus is not good for helices and strands. Due to the extra covalent bond, proline is already ‘pre-bend’, and thus good for turns. And turns tend to be at the surface. So, even though it is very hydrophobic, Pro often sits at the surface. We call this a forced marriage. *Except at the N-terminus, of course. ©CMBI 2001

P Pro Proline Bone and skin contain large amounts of proline/hydroxyproline Bone is a mixture of hydroxylapatite and collagen Collagen is unusual proline and hydroproline rich protein Hydroxylapatite is a calcium phosphate molecule Which protein is very rich in calcium, phosphate and proline: Casein! Cows milk is the most casein rich milk source known (much more than human, goat or sheep). A lot of milk ---  relationship to bone and skin development -  taller. But also other sources rich in the components above and contribute as well as individual differences in gene expression related to proline metabolism.

Q Gln Glutamine Glutamine is a large, polar residue. It is not very picky about its secondary structure but has a mild preference for the helix. It is isosteric with glutamic acid. ©CMBI 2001

R Arg Arginine Arginine is a big, hydrophilic, positively charged residue. It is not picky about its secondary structure. Its side chain contains a so- called guadinium group that is rigid. ©CMBI 2001

S Ser Serine Serine is a small, alcoholic residue of intermediate hydrophobicity. It is not too happy in helices and strands, but it loves to sit in turns. It often forms the active site of an enzyme together with histidine and aspartic acid. It is occasionally involved in metal (Ca) binding. ©CMBI 2001

T Thr Threonine Threonine is a small, alcoholic residue of intermediate hydrophobicity. It is beta- branched and thus good for beta strands. It doesn’t care about helices or turns. It is occasionally involved in metal (Ca) binding. ©CMBI 2001

V Val Valine Valine is a small hydrophobic residue. It is beta-branched and thus good for beta strands. Valine doesn’t care about helices, but it hates turns. It is isosteric with threonine. ©CMBI 2001

W Trp Tryptophan Tryptophan is the biggest residue. It is aromatic. Despite that the nitrogen in the five-ring is donor for hydrogen bonds, it is very hydrophobic. It doesn’t care about helices or turns, but it loves strands. Size matters. Its size determines that Trp is the most conserved of all residues. ©CMBI 2001

Y Tyr Tyrosine Tyrosine is a large, aromatic, alcoholic residue of intermediate hydrophobicity. It is not so happy in a helix, indifferent about turns, and it loves a strand. ©CMBI 2001