【正文】 y) 4 180,000,000 ~18,000 Saccharomyces cerevisiae (Yeast) 16 14,000,000 ~6,000 Zea mays (Corn) 10 2,400,000,000 ??? Genome Comparison 2022/6/2 109 Transcriptome ? plete collection of all possible mRNAs (including splice variants) of an anism. ? regions of an anism’s genome that get transcribed into messenger RNA. ? transcriptome can be extended to include all transcribed elements, including noncoding RNAs used for structural and regulatory purposes. 2022/6/2 110 Proteome ? the plete collection of proteins that can be produced by an anism. ? can be studied either as static (sum of all proteins possible) or dynamic (all proteins found at a specific time point) entity 2022/6/2 111 Review of Proteins ? Proteins: polypeptides with a three dimensional structure ? ? Primary structure – sequence of amino acids constituting polypeptide chain ? Secondary structure – local anization of polypeptide chain into secondary structures such as ? helices and ? sheets 2022/6/2 112 Review of Proteins ? Tertiary structure –three dimensional arrangements of amino acids as they react to one another due to polarity and interactions between side chains ? Quaternary structure – Interaction of several protein subunits 2022/6/2 113 Protein Structure ? Proteins: chains of amino acids joined by peptide bonds ? Amino Acids: – Polar (separate positive and negatively charged regions) – free C=O group (CARBOXYL), can act as hydrogen bond acceptor – free NH group (AMINYL), can act as hydrogen bond donor 2022/6/2 114 Protein Structure 2022/6/2 115 Protein Structure ? Many confirmations possible due to the rotation around the AlphaCarbon (C?) atom ? Confirmational changes lead to differences in threedimensional structure of protein 2022/6/2 116 Protein Structure ? Polypeptide chain has pattern of NC?C repeated ? Angle between aminyl group and C? is PHI (?) angle。 angle between C? and carboxyl group is PSI (?) angle 2022/6/2 117 Protein Structure 2022/6/2 118 Differences between .’s ? Difference between 20 amino acids is the R side chains ? Amino acids can be separated based on the chemical properties of the side chains: – Hydrophobic – Charged – Polar 2022/6/2 119 Differences between .’s ? Hydrophobic: Alanine(A), Valine(V), phenylalanine (Y), Proline (P), Methionine (M), isoleucine (I), and Leucine(L) ? Charged: Aspartic acid (D), Glutamic Acid (E), Lysine (K), Arginine (R) ? Polar: Serine (S), Theronine (T), Tyrosine (Y)。 Histidine (H), Cysteine (C), Asparagine (N), Glutamine (Q), Tryptophan (W) ? 2022/6/2 120 Secondary Structure 2022/6/2 121 Secondary Structures ? Core of each protein made up of regular secondary structures ? Regular patterns of hydrogen bonds are formed between neighboring amino acids ? Amino acids in secondary structures have similar ? and ? angles 2022/6/2 122 Secondary Structures ? Structures act to neutralize the polar groups on each amino acid ? Secondary structures tightly packed in protein core and a hydrophobic environment ? Each amino acid side group has a limited space to occupy therefore a limited number of possible interactions 2022/6/2 123 Types of Secondary Structures ?? Helices ?? Sheets ? Loops ? Coils 2022/6/2 124 ? Helix ? Most abundant secondary structure ? amino acids per turn ? Hydrogen bond formed between every fourth reside ? Average length: 10 amino acids, or 3 turns ? Varies from 5 to 40 amino acids 2022/6/2 125 ? Helix ? Normally found on the surface of protein cores ? Interact with aqueous environment – Inner facing side has hydrophobic amino acids – Outerfacing side has hydrophilic amino acids 2022/6/2 126 ? Helix ? Every third amino acid tends to be hydrophobic ? Pattern can be detected putationally ? Rich in alanine (A), gutamic acid (E), leucine (L), and methionine (M) ? Poor in proline (P), glycine (G), tyrosine (Y), and serine (S) 2022/6/2 127 ? Sheet 2022/6/2 128 ? Sheet ? Hydrogen bonds between 510 consecutive amino acids in one portion of the chain with another 510 farther down the chain ? Interacting regions may be adjacent with a short loop, or far apart with other structures in between 2022/6/2 129 ? Sheet ? Directions: – Same: Parallel Sheet – Opposite: Antiparallel Sheet – Mixed: Mixed Sheet ? Pattern of hydrogen bond formation in parallel and antiparallel sheets is different 2022/6/2 130 ? Sheet ? Slight counterclockwise rotation ? Alpha carbons (as well as R side groups) alternate above and below the sheet ? Prediction difficult, due to wide range of ? and ? angles 2022/6/2 131 Interactions in Helices and Sheets 2022/6/2 132 Loop ? Regions between ? helices and ? sheets ? Various lengths and threedimensional configurations ? Located on surface of the structure 2022/6/2 133 Loop ? Hairpin loops: plete turn in the polypeptide chain, (antiparallel ? sheets) ? More variable sequence structure ? Tend to have charged and polar amino acids ? Frequently a ponent of active sites 2022/6/2 134 Coil ? Region of secondary structure that is not a helix, sheet, or loop 2022/6/2 135 Secondary Structure 2022/6/2 136 6 Classes of Protein Structure 1) Class ?: bundles of ? helices connected by loops on surface of proteins 2) Class ?: antiparallel ? sheets, usually two sheets in close contact forming sandwich 3) Class ?/?: mainly parallel ? sheets with intervening ? helices。 may also have mixed ? sheets (metabolic enzymes) 2022/6/2 137 6 Classes of Protein Structure 4) Cla