Transcript Document

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/
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
Love hides in molecular structures.
Jim Morrison, Love Hides, from Absolutely Live, The Doors
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
Nucleic acid structure
DNA ----------> RNA --------------> Protein
Transcription
Translation
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.
Clicker question
What is the significance of the structure
of DNA?
1)
2)
3)
4)
It explains how genetic material is copied.
It explains how proteins are translated.
It explains how mutations occur.
It can be made into beautiful works of art.
Clicker question
Which part of the DNA structure explains
how DNA is replicated?
1)
2)
3)
4)
The sugar-phosphate backbone
The deoxynucleotides
The amino acids
The basepairs
Clicker question
Which part of the DNA structure explains
how DNA is replicated?
A)
B)
C)
D)
The sugar-phosphate backbone
The deoxynucleotides
The amino acids
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)
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/iss3/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 a-helices and b-sheets in
proteins, wasn’t infallible. But (important point here) he was thinking and
proposing solutions to important problems.
Triplet code
The Genetic Code-- it’s
(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?
Single stranded RNA can fold into complicated
3D shapes resulting
from intramolecular basepairing
07_05_RNA.jpg
Hairpin structures result from regions
of sequence that are complementary
to each other (inverted repeats).
Structure of a
ribozyme, an RNA
enzyme
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.
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.
1.45Å
C
1.33Å
N
C
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
Proteins are held together by noncovalent interactions
Figure 3-9
Clicker question: the type of interaction most likely to occur between a
glutamic acid residue and an arginine residue is…
1) Electrostatic
Glu
2) H-bond
Arg
3) VdW
4) Hydrophobic
Clicker question: the type of interaction most likely to occur between a
glutamic acid residue and an arginine residue is…
1) Electrostatic
Glu
2) H-bond
Arg
3) VdW
4) Hydrophobic
PROTEIN STRUCTURE
Primary structure: sequence
Secondary structure:
a-helix, b-sheet
Tertiary structure:
How the secondary
structural elements
are arranged to form
a compact structure.
(G S H S M R Y F Y T S . . .)
a-helix
a-helix
Antiparallel
b-sheets
Parallel
b-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
Different ways to depict a protein structure
Wire diagram
Ribbon diagram
Ball & stick of
featured area
Blue: positive
Red: negative
Space filling:
van der Waals
Surface
representation
(GRASP image)
Petsko G.A., Ringe, D., Protein Structure and Function 2004, figure 5-5, pg. 173.
Primary Structure:
Amino Acid Sequence
•
Enter Somethign
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
From Tertiary to Quaternary Structure:
Hemoglobin as an Example
•
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
Hemoglobin, Tertiary Structure
Hemoglobin, Quaternary Structure
Tetrameric Hemoglobin
Single Subunit
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 Baker’s 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. We’re 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!