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ProteinsProteins++

TranslatiTranslationon

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Amino acidsAmino acidsAmino acids are the basic structural units of proteins. All proteins in all organisms are constructed from 20 primary amino acids.

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The side chains of the amino acids (R) vary in size, shape, charge, bonding, composition, and reactivity.

Amino acids are distinguished from one another by their side chains.

Amino acidsAmino acids

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22 proteinogenic amino acids* = 20 primary amino acids** + pyrrolysine + selenocysteine

*proteinogenic amino acids = amino acids that are found in proteins and are encoded by a genetic code.**primary amino acids = found in all proteins in all organisms

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Zillions of nonproteinogenic amino acids, e.g., -naphthylalanine

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There are

2020

primary

amino acids.

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Amino acidsAmino acidsWith the exception of glycine (R = H), all amino acids can form mirror-image enantiomers around the carbon: levorotatory (L) and dextrorotatory (D). In proteins synthesized via translation of mRNA, only L-amino acids are used.

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•The smallest amino acid is Gly (molecular weight = 75). •The largest amino acid is Trp (molecular weight = 204). •Pro is an an imino acid.•Three amino acids (Phe, Tyr, Trp) have aromatic side chains. •Cys contains a sulfur atom.•Lys and Arg are positively charged at neutral pH.•Asp and Glu are negatively charged at neutral pH.•At pH = 6.0, ~50 percent of His are positively charged; at pH = 7.0, ~10 percent have a positive charge. •Gln and Asn are uncharged derivatives of glu and asp, respectively.

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Venn diagram showing the division of the 20 primary amino acids into overlapping categories according to size, polarity, charge, and hydrophobicity. Note that C appears in two distinct places, as reduced cysteine (CH) and as cystine (CS-S).

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Proteins: Four levels of Proteins: Four levels of structural organization:structural organization:

Primary structure

Secondary structure

Tertiary structure

Quaternary structure

11Primary structure = the linear amino acid sequence

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Secondary structure = spatial arrangement of amino-acid residues that are adjacent in the primary structure

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helix = A helical structure, whose chain coils tightly as a right-handed screw with all the side chains sticking outward in a helical array. The tight structure of the helix is stabilized by same-strand hydrogen bonds between NH groups and CO groups spaced at four amino-acid residue intervals.

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The -pleated sheet is made of loosely coiled strands are stabilized by hydrogen bonds between -NH and -CO groups from adjacent strands.

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An antiparallel β sheet. Adjacent β strands run in opposite directions. Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure.

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A parallel β sheet. Adjacent β strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.

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18Silk fibroinSilk fibroin

19Tertiary structure = three-dimensional structure of protein

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The tertiary structure is The tertiary structure is formed by the folding of formed by the folding of secondary structures by secondary structures by covalent and non-covalent covalent and non-covalent forces, such asforces, such as hydrogen hydrogen bondsbonds,, hydrophobic hydrophobic interactionsinteractions,, salt salt bridgesbridges between between positively and negatively positively and negatively charged residues, as well charged residues, as well asas disulfide bondsdisulfide bonds between pairs of between pairs of cysteines.cysteines.

21Quaternary structure = spatial arrangement of subunits and their contacts.

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Prosthetic group

Holoprotein

Holoproteins & Apoproteins

Apoprotein

Prosthetic groupHoloprotein

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Apohemoglobin = 2Apohemoglobin = 2 + 2 + 2

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Prosthetic group

HemeHeme

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Hemoglobin = Apohemoglobin + 4HemeHemoglobin = Apohemoglobin + 4Heme

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Sela M, White FH, & Anfinsen CB. 19591959. The reductive cleavage of disulfide bonds and its application to problems of protein structure. Biochim. Biophys. Acta. 31:417-426.

Christian B. AnfinsenChristian B. Anfinsen1916-19951916-1995

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Reducing agents: Ammonium thioglycolate (alkaline) pH 9.0-10Glycerylmonothioglycolate (acid) pH 6.5-8.2

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Oxidant

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Intrinsically unstructured proteins, often referred to as “naturally unfolded proteins” or “disordered proteins,” are proteins characterized by a lack of stable tertiary structure when the protein exists as an isolated polypeptide under physiological conditions in vitro.

Chouard T. 2011. Nature 471:151-153

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TranslationTranslationRNA Protein

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initiation: AUGinitiation: AUGmostlymostly

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initiationinitiation

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glycylalanine alanylglycine

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Genetic CodesGenetic Codes

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魚 yú fish

Transcription Translation

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translation = decoding

Conversion of information from one language into another.

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George GamowThe Diamond Code (1956)

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translation = decodingConversion of information from a language with a 4-letter alphabet (RNA) into one with a 20-letter alphabet (protein). What should the conversion minimal size (codon) be?

1 letter codons 1 letter codons 4 4 possibilitiespossibilities2 letter codons 2 letter codons 16 16 possibilitiespossibilities3 letter codons 3 letter codons 64 64 possibilitiespossibilities

49 Marshall Nirenberg (right) and Heinrich Matthaei

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Rules of Translation: The “Universal” Genetic CodeRules of Translation: The “Universal” Genetic Code

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AAAAACGAA lys asn glu

Nonoverlapping CodeNonoverlapping Code

AAAAACGAA lys lys

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AAAAACGAA lys asn glu

Comaless CodeComaless Code

AAAAACGAA lys thr

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CTACTCCTG leu leu leu

Degenerate CodeDegenerate Code

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CTACTCCTG leu leu leu

Unambiguous CodeUnambiguous Code

gly tyr ser

With rare exceptions the genetic code is

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Polysemous = possessing a multiplicity of meaning

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six

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Rules of Translation: The Rules of Translation: The “Universal”“Universal” Genetic Code Genetic Code StandarStandardd

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The Vertebrate Mitochondrial Genetic CodeThe Vertebrate Mitochondrial Genetic Code

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Last Update in NCBI (July 7, 2010):Last Update in NCBI (July 7, 2010):

17 genetic codes

1 standard 16 alternative

5 nuclear8 mitochondrial1 both nuclear& mitochondrial

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

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In some organisms, some In some organisms, some codons may never appear codons may never appear in protein-coding in protein-coding genes. These are called genes. These are called absentabsent codonscodons. .

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In some organisms, some codons In some organisms, some codons may not have appropriate tRNA may not have appropriate tRNA to pair with. These codons are to pair with. These codons are called called unassignedunassigned codonscodons. .

Examples: Examples:

Codons AGA and AUA are Codons AGA and AUA are unassigned in unassigned in Micrococcus Micrococcus luteusluteus. .

Codon CGG is unassigned in Codon CGG is unassigned in Mycoplasma capricolumMycoplasma capricolum. .

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Unassigned Unassigned oror Hungry Hungry CodonsCodons differ from differ from Stop Stop CodonsCodons by not being by not being recognized by release recognized by release factors. Thus, upon factors. Thus, upon encountering an encountering an unassigned codon, unassigned codon, translation stalls, and translation stalls, and the polypeptide remains the polypeptide remains attached to the attached to the ribosome. ribosome.

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Flow of information: Flow of information:

DNA RNA Protein

replication

transcription translation

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Flow of information: Flow of information:

DNA RNA Protein