No lecture Wed Apr 6 so students can participate in the Student-Faculty Conference We encourage you to attend the SFC on Wed. 4/6 starting at 11am in Ramo

No lecture Wed Apr 6 so students can participate in the Student-Faculty Conference We encourage you to attend the SFC on Wed. 4/6 starting at 11am in Ramo Auditorium. Please check the full SFC schedule at http://www.ugcs.caltech.edu/~arc/ http://www.ugcs.caltech.edu/~arc/ PJB will still have office hours at 2pm on Wednesday.

An experimental method to determine macromolecular structures: X-ray Crystallography Crystal Growth X-ray Data Electron Density Protein Model

Macromolecular structure Macromolecules are created by covalently linking small molecules (monomers or subunits) into long chains or polymers. Sugars are energy sources for cells. Proteins catalyze reactions and perform MANY other functions in cells. Nucleic acids (DNA, RNA) store and transmit hereditary information. Little Alberts, Figure 2-27 Love hides in molecular structures. Jim Morrison, Love Hides, from Absolutely Live, The Doors

Nucleic acid structure DNA ----------> RNA --------------> Protein The information for the amino acid sequence of each protein is stored in DNA as a code. DNA is transcribed into RNA, which serves as a messenger that is translated into protein. Transcription Translation

What is the significance of the structure of DNA? 1)It explains how genetic material is copied. 2)It explains how proteins are translated. 3)It explains how mutations occur. 4)It can be made into beautiful works of art. Clicker question

Which part of the DNA structure explains how DNA is replicated? 1)The sugar-phosphate backbone 2)The deoxynucleotides 3)The amino acids 4)The basepairs Clicker question

Which part of the DNA structure explains how DNA is replicated? A)The sugar-phosphate backbone B)The deoxynucleotides C)The amino acids D)The basepairs It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. (J. Watson & F. Crick, 1953, Nature 171: 737-738) Clicker question

DNA is made from four nucleotide building blocks: Adenine (A), Thymine (T), Cytosine (C), Guanine (G) Little Alberts, Figure 2-25

DNA structure video

Watson and Crick deduced the structure of DNA from this diffraction image What is the significance of the X? Find out at this website: http://www.pbs.org/wgbh/nova/photo51/ Find out more about Rosalind Franklin, the scientist who recorded this diffraction pattern, in this article: "Rosalind Franklin and the Double Helix," by Lynne Osman Elkin, Physics Today, March 2003 http://www.physicstoday.org/vol-56/iss- 3/p42.html

The structure of DNA explains how genetic information is copied Each strand of the DNA double helix is complementary to its partner strand, so each can act as a template for synthesis of a new complementary strand (semi-conservative replication). Base-pairing allows a simple way for cells to pass on their genes to descendents.

Incorrect DNA model Even Linus Pauling, a brilliant chemist who discovered -helices and -sheets in proteins, wasnt infallible. But (important point here) he was thinking and proposing solutions to important problems.

Triplet code

The Genetic Code-- its (pretty much) universal 64 triplets encode 20 amino acids (most amino acids are encoded by more than one triplet) plus a termination signal (3 different stop codons).

What about the structure of RNA?

07_05_RNA.jpg Single stranded RNA can fold into complicated 3D shapes resulting from intramolecular basepairing Structure of a ribozyme, an RNA enzyme Hairpin structures result from regions of sequence that are complementary to each other (inverted repeats).

What do proteins do? Catalysis -- enhancement of reaction rates (e.g., a polymerase makes polymers from monomers) Transport and storage (e.g., hemoglobin) Immune protection (e.g., antibodies) Control of gene expression (e.g., repressors) Mechanical support (e.g., collagen in skin and bone)

What is an enzyme? Enzymes are proteins* that catalyze (accelerate) chemical reactions. Many of their names end in ase ( e.g., polymerase, kinase, protease). Substrate: molecule at the beginning of the reaction. Product: molecule at the end of the reaction. The activity of an enzyme is determined by its 3-D structure. Enzymes lower the activation energy for a reaction. *Some RNA molecules can act as enzymes to catalyze reactions, but most enzymes are proteins.

Proteins we will discuss in Bi 1 DNA-binding proteins Enzymes, including DNA and RNA polymerase, ribosomes* HIV proteins Antibodies and immune system proteins Cytoskeletal proteins (actin, tubulin) Almost every time we discuss a function that is carried out in a cell or a virus, it is done by a PROTEIN. *Ribosomes contain proteins, but their catalytic activies are carried out by RNA

Proteins are made from amino acids linked together by planar peptide bonds

Clicker question: Peptide bonds are planar because the N-C bond has partial double bond character. Linus Pauling (Caltech) provided evidence for this when he was able to show that 1) A trans conformation is favored for the N-C dihedral angle for most amino acids. 2) The distance measured for a peptide bond was shorter than expected for a typical C-N single bond. 3)N-C bonds break spontaneously in aqueous solvents. 4)Hemoglobin contains many double bonds.

C N 1.45 1.33 C Clicker question: Peptide bonds are planar because the N-C bond has partial double bond character. Linus Pauling (Caltech) provided evidence for this when he was able to show that 1) A trans conformation is favored for the N-C dihedral angle for most amino acids. 2)The distance measured for a peptide bond was shorter than expected for a typical C-N single bond. 3)N-C bonds break spontaneously in aqueous solvents.

Properties of the 20 amino acids in proteins See also http://www.imb-jena.de/IMAGE_AA.html and p. 74-75 of Essential Cell Biology

Figure 3-9 Proteins are held together by noncovalent interactions

Clicker question: the type of interaction most likely to occur between a glutamic acid residue and an arginine residue is 1) Electrostatic2) H-bond3) VdW 4) Hydrophobic Glu Arg

PROTEIN STRUCTURE Primary structure: sequence ( G S H S M R Y F Y T S...) Secondary structure: -helix, -sheet Tertiary structure: How the secondary structural elements are arranged to form a compact structure.

-helix

Antiparallel -sheets Parallel

-sheet

Color conventions for amino acids www.cryst.bbk.ac.uk/PPS95/ course/3_geometry/peptide1.html See pages B8-B9 at end of your textbook

Petsko G.A., Ringe, D., Protein Structure and Function 2004, figure 5-5, pg. 173. Different ways to depict a protein structure Wire diagram Ribbon diagram Ball & stick of featured area Space filling: van der Waals Surface representation (GRASP image) Blue: positive Red: negative

Enter Somethign Primary Structure: Amino Acid Sequence

Model of HIV protease http://mgl.scripps.edu/projects/tangible_models/movies

Tertiary Structure: An Example of an All-Alpha Protein, Hemoglobin Subunit Rotated 90 Degrees

Tertiary Structure: An Example of an All-Beta Protein, Flu Virus Neuraminidase 1) Rotate 90 Degrees

Tertiary Structure: An Example of an Alpha/Beta Protein, Triose Phosphate Isomerase 1) Rotate 90 Degrees

Tertiary Structure: An Example of an Alpha + Beta Protein, TATA Binding Protein 1) Rotate 90 Degrees

Quaternary structure -- the relative arrangement of two or more individual polypeptide chains Protein assemblies can contain one type of polypeptide (homo-oligomer) or multiple types (hetero-oligomer) Example: Hemoglobin (oxygen carrier in blood) Hemoglobin is a hetero-tetramer composed of two alpha subunits and two beta subunits From Tertiary to Quaternary Structure: Hemoglobin as an Example

Hemoglobin, Tertiary Structure

Hemoglobin, Quaternary Structure Single Subunit Tetrameric Hemoglobin

Clicker question: A good design for a stable folded protein is 1)A polar/charged core with mostly nonpolar residues on the surface. 2)A nonpolar core with mostly polar/charged residues on the surface. 3)An even mix of polar/charged and nonpolar residues in the core and on the surface. 4)Fatty acids on the inside, ribonucleotides on the outside. 5)Ralph Lauren.

Clicker question: A good design for a stable folded protein is A) A polar/charged core with mostly nonpolar residues on the surface. B) A nonpolar core with mostly polar/charged residues on the surface. C)An even mix of polar/charged and nonpolar residues in the core and on the surface. D)Fatty acids on the inside, ribonucleotides on the outside. E)Ralph Lauren.

The Protein Folding Problem: the sequence of a protein cannot (yet) be used to predict its 3D structure ?

Protein Structure Prediction Critical Assessment of techniques for Structure Prediction (CASP 9) -- a competition For more information or to enter, see http://predictioncenter.org/ Winners earn an automatic A+ in Bi 1 (retroactively, if necessary)

Foldit New Nature Video - Foldit: Biology for gamers - August 04, 2010 http://blogs.nature.com/news/thegreatbeyond/20 10/08/new_nature_video_foldit_biolog.html From David Bakers webpage: (http://depts.washington.edu/bakerpg/drupal/) Foldit is a revolutionary new computer game enabling you to contribute to important scientific research. Join this free online game and help us predict the folds of unsolved proteins as well as designing new proteins to cure diseases. Were collecting data to find out if humans' pattern-recognition and puzzle-solving abilities make them more efficient than existing computer programs at pattern-folding tasks. If this turns out to be true, we can then teach human strategies to computers and fold proteins better than ever!

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No lecture Wed Apr 6 so students can participate in the Student-Faculty Conference We encourage you to attend the SFC on Wed. 4/6 starting at 11am in Ramo