Announcements • Quiz today over Chpt 2 of Phillips et al. • Written HW due Wednesday • Example of your 12 minute Lectures Proteins (quick review) RNA Proteins (The Ribosome, tRNA) Next time: the midterm, how to choose paper for research project Quiz 1. The Cell Interior is a crowded place. This means that the average spacing between molecules is: a. Much less than the dimensions of the average molecule. b. About equal to the dimensions of the average molecule. c. Much greater than the dimensions of the average molecule. 2. Membrane-bound organelles, are defining features of eukaryotic cells that differentiate these cells from bacteria and archea. Among the roles of such membranes are to: a. Genome management Nucleus b. Energy Generation Mitochondria, Cell membrane c. Protein synthesis. E.R. and/or Golgi Apparatus What are the organelles associated with a, b, and c? 3. Amino acids have a side chain, sometime called “R” (see picture). The side chains are often grouped according to their physical properties. a) How are they classified? (I’m looking for three words) Hydrophobic, Polar (Hydrophilic), Charged As an example: Lysine has a CH-NH3+; Phenylalanine has a CH2-Benzene-ring. L-Charged, Outside A)Which tend to be inside a protein? P-Hydrophobic, Inside B)Which tend to be on the outside of proteins? Quick Review Linear sequence of ~ 20 amino acids Can get enormous diversity and function with Proteins Figure 5.UN01 Amino Acid Structure Side chain (R group) (110 g/mole) Amino group carbon Carboxyl group 20 different R groups Hydrophobic (non-polar; greasy) Hydrophilic (polar; non-greasy) Charge: positive, neutral, negatively Determines where they go: inside vs. outside Figure 5.16 Amino Acid Structure—20 Diff. R Nonpolar side chains; hydrophobic Side chain (R group) Glycine (Gly or G) Methionine (Met or M) Alanine (Ala or A) Valine (Val or V) Phenylalanine (Phe or F) Leucine (Leu or L) Tryptophan (Trp or W) Isoleucine (Ile or I) Proline (Pro or P) Polar side chains; hydrophilic Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Aspartic acidGlutamic acid (Asp or D) (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Secondary Structure -helix, b-sheets -helix, b-sheets depends on specific amino acids • Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents • These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions • Strong covalent bonds called disulfide bridges may reinforce the protein’s structure © 2011 Pearson Education, Inc. Figure 5.20f Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge (Covalent bond) Ionic bond Polypeptide backbone (Not gone over in lecture but presented here.) Figure 5.20b 4 layers of Protein Structure Tertiary structure Secondary structure Quaternary structure helix Hydrogen bond b pleated sheet (b arrow toward b strand carboxyl end) Hydrogen bond Transthyretin polypeptide Transthyretin protein Size of proteins 10kD to 100kD to over a million Recall aa = 110 D…say 100D 10kD=100aa Figure 5.18 Alternative Representations Groove Groove (a) A ribbon model (b) A space-filling model • The sequence of amino acids determines a protein’s threedimensional structure • A protein’s structure determines its function © 2011 Pearson Education, Inc. Protein Structure and Function • A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape © 2011 Pearson Education, Inc. Figure 5.19 Antibody protein Protein from flu virus Figure 5.20d Sickle-Cell Disease: A Change in Primary Structure • A slight change in primary structure can affect a protein’s structure and ability to function • Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin © 2011 Pearson Education, Inc. Figure 5.21 Sickle Cell Anemia Sickle-cell hemoglobin Normal hemoglobin Primary Secondary Quaternary Structure and Tertiary Structure Structures 1 2 3 4 5 6 7 Function Red Blood Cell Shape Molecules do not Normal hemoglobin associate with one another; each carries oxygen. b subunit b 10 m b 1 2 3 4 5 6 7 Exposed Sickle-cell Molecules crystallize hydrophobic hemoglobin into a fiber; capacity region to carry oxygen is reduced. b subunit b b 10 m Why does sickle cell anemia still exist? It is clearly disadvantageous to have disease; make probability of reproducing less likely. Recall you’re diploid—have two copies of each gene. If have both SS, then you have anemia. If both genes unmutated: “normal”. If heterozygote, (one “good”, one “bad”) then have certain advantages. If mother/father have SS and NN, probability of kid having SS? NN? SN? Advantage: More resistant to malaria. How Proteins are made DNA RNA Proteins Central Dogma of Molecular Biology DNA: linear series of 4 nucleotides (bases): A,T,G,C Double-stranded Transcription [DNA & RNA similar] RNA: linear series of 4 nucleotides (bases): A,U,G,C Mostly single-stranded Translation [RNA & Proteins different] Proteins: linear series of 20 amino acids: Met-Ala-Val-… each coded by 3 bases amino acid AUG Methionine; GCU Alanine; GUU Valine Proteins are 3-D strings of linear amino acids Do everything: structure, enzymes… http://learn.genetics.utah.edu/units/basics/transcribe/ RNA has 3 different uses 3 different names, (mRNA, tRNA, rRNA) A key element of the central dogma of molecular biology: that DNA makes RNA makes protein 1. Messenger RNA (mRNA) [~copy of DNA] 2. transfer RNA (tRNA) [binds to amino acid and codon for mRNA] 3. ribosomal RNA (rRNA) [Makes up Ribosome, along with protein. Has catalytic activity– can form peptide bond. RNA is catalytic!] Focus on RNA Proteins http://en.wikipedia.org/wiki/Messenger_RNA Ribosome A key element of the central dogma of molecular biology: that DNA makes RNA makes protein 5’ 3’ Takes the sequence in mRNA and produces a polypeptide (protein) Stages in translation: Initiation, Elongation, Termination, Recycling We’ll learn how to measure these things– nanometer scale, sub-second time resolution E.M. and x-ray crystallography, Fluorescence Ribosome is made of two subunits 30S and 50S sub-units The smaller subunit binds to the mRNA, while the larger subunit binds to the tRNA and the amino acids. When a ribosome finishes reading a mRNA, these two subunits split apart. 20 nm 20 nm The assembly process involves the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs, as well as assembly of those rRNAs with the ribosomal proteins. Transfer RNA (tRNA) CCA tail binds to amino acid AminoacylationtRNA synthetase (depends on ATP) Tertiary structure of tRNA ds RNA Anticodon in black 1st base often modified-allow wobble Its primary structure (including bases which have been methylated), its secondary structure (usually visualized as the cloverleaf structure), and its tertiary structure (all tRNAs have a similar L-shaped 3D structure that allows them to fit into the P and A sites of the ribosome). http://en.wikipedia.org/wik i/Transfer_RNA Translation (RNA Protein) http://www.youtube.com/watch?fea ture=endscreen&NR=1&v=Ikq9Ac BcohA Slight more detailed view of Protein Synthesis http://www.youtube.com/watch?v=1PSwhTGFMxs &feature=endscreen&NR=1 Class evaluation 1. What was the most interesting thing you learned in class today? 2. What are you confused about? 3. Related to today’s subject, what would you like to know more about? 4. Any helpful comments. Answer, and turn in at the end of class.