CHEM 105:  CHEMISTRY AND SOCIETY

Lab 4:  Molecular Modeling  - Proteins, DNA, and the Central Dogma of Biology

Introduction

In this �dry� lab you will 

You will see several of the functional groups in proteins and DNA that we have studied in class.

Amino Acids

The monomer in a protein is called an amino acid, a completely different kind of molecule than a nucleotide.   There are twenty different naturally occurring amino acids that differ in one of the 4 groups connected to the central carbon.  In an amino acid, the central (alpha) carbon has an amine group (RNH2), a carboxylic acid group (RCOOH), (both groups you studied last week) an H, and an R group attached to it.

Jmol:  Amino Acids:  Structures

Proteins

The amino acid (monomers) react covalently to form a long chain called a protein (a polymer).  The linear sequence of a protein can be depicted in many ways, as shown below.

The actual linear sequence of a protein is called its primary (1o) structure.

 

 

The protein chain can form regular repetitive secondary (2o) structures called alpha helices and beta sheets through the formation of H bonds between the backbone amide H (δ+) of one amino acid and the backbone carbonyl O (δ-) of another amino acid in the protein.  These H bonds are all among main chain atoms in the backbone, not among side chains.

The protein ultimately forms a unique 3D shape, which usually contains some alpha helices and beta sheets. This 3 D structure is called the tertiary (3o) structure of the protein.

 In the Chime models below, use the mouse controls to rotate the molecule.  (Also shift L-mouse click will change the size of the molecule).  Click on the command in the right hand frame to change the rendering of the proteins.  The cartoon view allows a simple way to interpret the overall structure of the main chain.

Lab Exercise 1:  View the following models illustrating aspects of protein structure

Jmol: Alpha Helices of Proteins - Observe the intrastrand H bond holding the helix together.  /Click on the sequential commands in the left window to view the molecule with different renderings.

Jmol: Twisted Beta Sheets  of Proteins - Observe the interstrand H bonds holding the structure together.

Jmol:  Beta Barrel of Proteins - Observe the inter-strand H bonds holding the structure together

Jmol:  Myoglobin- an oxygen binding protein - Observe the predominately alpha-helical nature of the protein

Jmol:  Superoxide Dismutase - a protein catalyst (enzyme)  that detoxifies the body of toxic oxygen byproducts and which high level of the protein have been associated with longer life spans.  Observe the predominate beta sheet structure of the protein.

Jmol: Triose phosphate isomerase - an enzyme involved in sugar metabolism

Lab Exercise 2: View the following models illustrating protein:small molecule binding interactions.

Protein-Molecule Interactions

Each unique protein sequence (of a given length and sequence of amino acids) folds to a unique 3D shape.   Not only do proteins have unique shapes, but they also have unique nooks and crannies and pockets which allow them to bind other molecules.  Binding (through non-covalent intermolecular forces or through covalent modification of proteins such as through phosphorylation) of other molecules to proteins initiates or terminates the function of the protein, much like an on/off switch.  The example below show different protein structures, some of which have small molecules or large molecules (like DNA) bound to them.   You will now view interactive displays of proteins interacting with molecules like DNA and drugs using Chime.  The interactions between drugs and proteins are mediated by intermolecular forces (like H  bonds, etc).

Chime: 1.  Protein: Antiviral Drug Complex:  1HSG:  Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. 

Chime:  2.  Protein:DNA Complex:  A bacterial virus (lambda) and an inhibitor protein

Chime: 3.  Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol.  The Hsp90 molecular chaperone is a protein that helps other proteins to fold to their correct state.  

Chime: 4.  Binding of the leech protein hirudin to thrombin, the blood clotting protein. Chain I is the hirudin protein found in the saliva of leeches.  The hirudin molecule is a small protein that lies in a grove in thrombin, preventing thrombin from clotting blood.

Structure of DNA

DNA is a polymer, consisting of monomers call nucleotides.  The monomer contains a simple sugar (deoxyribose), a phosphate group, and a cyclic organic group that is a base (not an acid).  Only four bases are used in DNA, which we will abbreviate, for simplicity, as A, G, C and T.  These 4 monomers contrast to the 20 monomoers (amino acids) of proteins.  The polymer consists of a sugar - phosphate - sugar - phosphate backbone, with 1 base attached to each sugar molecule.   DNA can exist as single-stranded (ss) structure (with one sugar-phosphate backbone), a double-stranded (ds) structure (with two sugar-phosphate backbones which bind to each other through their bases) , or mixed forms. It is actually a misnomer to call dsDNA a molecule, since it really consisted of two different, complementary strands held together by intermolecular forces called hydrogen bonds.  These forces are like the "velcro" attractions that would bind two objects with opposite types of velcro to each other.  dsDNA varies in length (number of sugar-phosphate units connected), base composition (how many of each set of bases) and sequence (the order of the bases in the backbone.  You already know the double-helical nature of double-stranded DNA.  It has become a cultural icon.  This twisted linear duplex is much simpler than the convoluted 3D structures of the more complicated proteins.  The links links below will help you understand the properties of DNA.

Lab Exercise 3:  View the following DNA structures, by selecting the appropriate prompts to change the rendering of the structures.

Jmol:  double-stranded DNA.

Jmol: DNA: Strands, Helical Backbone

Jmol: DNA:  Ends and Antiparallelisms

Jmol: DNA:  Ends and Antiparallelisms

 

Central Dogma of Biology:

DNA is the carrier of genetic information in organisms.  What does that mean?   Large molecules in organism can have many functions: they can provide structure,  act as catalyst for chemical reactions,  serve to sense changes in their environment (leading to immune responses to foreign invaders and to neural responses to stimuli such as light, heat, sound, touch, etc) and provide motility.  DNA really does none of these things.  Rather you can view it as an information storage system.   The information must be decode to allow the construction of other large molecules.   The other molecules are usually proteins, another class of large polymers in the body. 

Chromosomes are located in the nucleus of a cell.  DNA must be duplicated in a process called replication before a cell divides.  The replication of DNA allows each daughter cell to contain a full complement of chromosomes.  The actual information in the DNA of chromosomes is decoded in a process called transcription   through the formation of another nucleic acid, ribonucleic acid or RNA.  The information from the DNA, now in the form of a linear RNA sequence, is decoded in a process called translation, to form a protein, another biological polymer.    

In contrast to the complementarity of DNA and RNA (1 base in RNA complementary to 1 base in DNA), there is not a 1:1 correspondence between a base (part of the monomeric unit of RNA) in RNA to the monomer in a protein. After much work it was discovered that a contiguous linear sequence of 3 nucleotides in RNA is decoded by the molecular machinery of the cytoplasm with the result that 1 amino acid is added to the growing protein.  Hence a triplet of nucleotides in DNA and RNA have the information for 1 amino acid in a protein.  That there was not a 1:1 correspondence between nucleotides in nucleic acids and amino acids in proteins was evident long ago since there are only 4 different DNA monomers (with A, T, G, and C) and 4 different RNA monomers (with A, U, G, and C) but there are 20 different amino acid monomers that compose proteins.   Each amino acid is specified by a particular combination of three nucleotides in RNA.  The three bases are called a codon.  The Genetic Code consists of a chart which shows what triplet RNA sequence or codon in mRNA codes for which of the 20 amino acids.  One of the codon codes for no amino acids and serves to stop the synthesis of the protein from the mRNA sequence. The genetic code is shown below:

GENETIC CODE

For a given gene, only one strand of the DNA serves as the template for transcription.  An example is shown below.   The bottom (blue) strand in this example is the template strand, which is also called the minus (-) strand,or the sense strand. It is this strand that serves as a template for the mRNA synthesis. The enzyme RNA polymerase sythesizes an mRNA in the 5' to 3' direction complementary to this template strand. The opposite DNA strand (red) is called the coding strand, the nontemplate strand, the plus (+) strand, or the antisense strand. 

The easiest way to find the corresponding mRNA sequence (shown in green below) is to read the coding, nontemplate, plus (+), or antisense strand directly in the 5' to 3' direction substituting U for T.  Find the triplet in the coding strand, change any T's to U's, and read from the Genetic Code the corresponding amino acid that would be incorporated into the growing protein.   

5'  T G A C C T T C G A A C G G G A T G G A A A G G  3'
3'  A C T G G A A G C T T G C C C T A C C T T T C C  5'
5'  U G A C C U U C G A A C G G G A U G G A A A G G  3'
Lab Exercise 4:  View the triplet base in DNA, the codon in the RNA, and the corresponding amino acid.

Chime Molecular Modeling: the Genetic Code

 

CHEM 105: Chemistry and Society

Report for Lab 4:  Molecular Modeling 2 - Central Dogma of Biology 

NAMES:  _____________       _______________

Lab Exercise 1: 
 
Write a few sentences describing the salient features of the following models that you viewed today.

a.  alpha helices

 

b.  beta barrel

 

c.  myoglobin

 

d.  superoxide dismutase

 

e.  triose phosphate isomerase

 

Lab Exercise 2: 

Write a few sentences describing the salient features of the following models that you viewed today.:

  1. Protein: Antiviral Drug Complex:  1HSG:

  2. Protein/DNA complex

  3. Protein/Radiciol (antitumor, antibiotic) complex

  4.  Thrombin:Hirudin complex

Lab Exercise 3: 

  1. Draw the Lewis structure of the sugar phosphate backbone.  Include formal charges.  Hypotheisze about the charge on the part of a protein that might bind to the dsDNA backbone.

 

  1. State the main difference between a GC and an AT base pair

 

Lab Exercise 4: 

Central Dogma of Biology

Below is a section of DNA which codes for part of a protein. The bottom (blue) strand in this example is the template strand, which is also called the minus (-) strand,or the sense strand. It is this strand that serves as a template for the mRNA synthesis. The enzyme RNA polymerase sythesizes an mRNA in the 5' to 3' direction complementary to the template strand. The opposite DNA strand (red) is called the coding strand, the nontemplate strand, the plus (+) strand, or the antisense strand. 

            1   2     3                         4
MUTATIONS:  G   A     T                         T
5'  C C C C T G G A A C A G T G G A C A G C A G G A  3'
3'  G G G G A C C T T G T C A C C T G T C G T C C T  5'
 

a. Write the mRNA sequence. Use the genetic code found below.

 

b. Write the amino acid sequence.

 

c. Consider the mutations shown in the top line. Suppose the single mutation 1 (T - G) occurs in the 5' to 3' strand, with a concomitant change in the template strand.  What is new amino acid in the mutant compared to the normal or wild type (WT)?    Mutations can causes changes in the folding of the protein and its function (if they occur at the active site).  What might happen to the new protein if the original amino acid was buried inside the protein? If it was exposed on the surface? Remember that the surface would include areas in the active or binding site or outside of the region as illustrated in this link.

mRNA sequence of mutant  WT  aa:  _______  to Mutant aa:  __________
Effect if WT aa buried: 

 

 

 Effect if WT aa on surface:

 

 

 

 d. Repeat (c), but with mutation 2 instead.

mRNA sequence of mutant  WT  aa:  _______  to Mutant aa:  __________
Effect if WT aa buried: 

 

 

 Effect if WT aa on surface:

 

 

 

 e. Repeat (c), but with mutation 3 instead.

mRNA sequence of mutant  WT  aa:  _______  to Mutant aa:  __________
Effect if WT aa buried: 

 

 

 Effect if WT aa on surface:

 

 

 

 f. Repeat (c), but with mutation 4 instead.

mRNA sequence of mutant  WT  aa:  _______  to Mutant aa:  __________
Effect if WT aa buried: 

 

 

 Effect if WT aa on surface: