Amino Acids - Complex Carbohydrate Research Center

Amino Acids - Complex Carbohydrate Research Center

Amino Acids and the Peptide Bond Lance Wells Biochemistry & Molecular Biology, CCRC [email protected] All lecture slides and papers for Thursday are available at: Learning Objectives: Know your 20 standard AAs Be able to classify based on side chain: ionizable,

aliphatic, aromatic, sulfur-containing, polar, nonpolar, etc.. Be able to draw a peptide bond and understand the amide character Be aware of PTMs Appreciate that function of proteins are dictated in large part by side chain properties of AAs /blog/ central-dogma-genetics-incomplete_id %3D904

Four Main Families of Biomolecules in Cells Nucleic Acids (DNA and RNA) Innate / Genetic Proteins Glycans Acquired / Metabolic

Lipids Modified from Marth, Nature Cell Biology 10, 1015-16 (2008) What imparts structure and function to proteins? Amino Acids: The building blocks of proteins pK2 pK1

amino acids because of the carboxylic and amino groups pK1 and pK2 respectively pKR is for R group pKs pK1 2.2 while pK2 9.4 In the physiological pH range, both carboxylic and amino groups are completely ionized Amino acids are Ampholytes They can act as either an acid or a base They are Zwitterions or molecules that have both

a positive and a negative charge Acid - Base properties of amino acids [A - ] pH pK log [HA] Isoelectric point: the pH where a molecule carries no net electrical charge

Amino acids are the building blocks of proteins Three major parts: carboxyl group, amino group, and side chain. Central C atom called alpha carbon. Amino acids can differ in their side chains (R). The alpha carbon is a chiral

center. (except for one amino acid) L-form found almost exculsively in proteins (CORN) Peptide bonds Proteins are sometimes called polypeptides since they contain many peptide bonds +

H3N R1 O C OH C +

H H R2 O N C O-

H H + H3N C R2 O

R1 O C H C N C

H H C O- + H2O Amide character in the peptide bond

Since the peptide bond is also an amide it also undergoes resonance. + H3N R2 O R1 O C


C O- Therefore, peptides are rigid due to resonance around the amide bond, having 40% double-bond character. This restricts the rotation due to delocalization of electrons and overlap of the O-C-N orbitals. Amino acids can form peptide

bonds Amino acid residue peptide units dipeptides tripeptides oligopeptides Proteins are molecules that consist of one or more

polypeptide chains polypeptides Peptides are linear polymers that range from ~8 to 4000 amino acid residues How many different naturally occurring amino acids are there in most species encoded by the genome? Linear arrays of amino acids can

make a huge number of molecules Consider a peptide with two amino acids AA1 20 AA2 x AA1

20 x 20 = 400 different molecules AA2 AA3

20 x 20 = 8000 different molecules For 100 amino acid protein the # of possibilities are: 20100 1.27 x10130 The total number of atoms in the universe is estimated at

4x10 80 Amino Acids If you want to be a protein biochemist you must know (or if you just want to get a good grade on test): Their names Their structure Their three letter code Their one letter code

Their ionization properties Their hydrophobicity and size Their hydrogen bonding properties Their other chemical properties such as ability to be post-translationally modified Why you need to know your AAs and their properties? Which AA is not really an AA but an imino acid? Non-polar R-groups tend to be

buried in the cores of soluble proteins Myoglobin Blue = non-polar R-group Red = Heme The Bricks that make up the hydrophobic core and contribute significantly to folding (hydrophobic interactions)

Polar, non-charged amino acids Cystine consists of two disulfide-linked cysteine residues Important In Protein Folding And Structure

Beyond 20AAs for Expanded Functionality -Genetic code (reading stop codons as AAsThursday) Selenocysteine and Pyrrolysine -Post-translational Modifications -Binding of Cofactors (later lectures) Gene Ultimate Gene Products

Functional Diversity Genome Sequencing RNA-Seq Traditional Proteomics Functional

Proteomics Protein Modified Protein mRNA Genomic DNA -P exon 1

exon 2 exon 3 -O-GlcNAc -P -Ub -P

-O-GlcNAc -O-GlcNAc Transcriptional Regulation Alternative Splicing, Cell Type Specific Expression, etc. Translational Regulation Post-translational Regulation Masking, mRNA Modification by Proteases, O-GlcNAc, Stability etc.

Phosphate, Ubiquitin, etc. Lots, and lots, of PTMs Post-translational Modification of Amino Acids (just a few examples of impact) Phosphorylation (Typically Ser, Thr, Tyr) Glycosylation (Typically Asn, Ser, Thr)

gain of charge, bindin solubility, stability, binding Acetylation/Acylation/Methylation (N-term, Lys, Arg) loss of charge, stability Lipidation/prenylation (Typically Cys) membrane anchoring

Ubiquitination/Sumoylation (Lys) degradation, signalin

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