Download Introduction to Protein Structure

AGR2451 Lecture 2 - M. Raizada
-Pick-up questionnaire at the front; results from last week
-Did you review your notes within 24 hours??
-15 minute meetings
-Reading for this week on reserve in the library:
Introduction to Protein Structure (pp. 3-12)
Review of Previous Lecture
1. Definition of science.
.
2. What is the chemical basis of life and why?
-water
-hydrophilic and hydrophobic atoms and
their functions (eg. membrane layer)
3. Why were N, O, P, S used? Unpaired electrons are critical to
Hydrogen bonding, which is critical for proteins, DNA and RNA to
function.
4. What is life?
Slide 2.1
Lecture 2 - An Introduction to Proteins
How is life organized?
1. evolution chose proteins to do the work of life.
(DNA is only the set of instructions to make proteins.)
2. What do proteins do?
-A. Structural proteins make large structures (eg. microtubule cables
to pull chromosomes apart during mitosis/meiosis)
protein
cables
From Biochemistry and Molecular Biology of Plants
(W.Gruissem, B. Buchanan and R.Jones p.236
ASPP, Rockville MD, 2000
-B. Enzymes - catalyze biochemical reactions - the key to life demo
Rather than 2 reactive molecules trying to “find each other”
by random diffusion, an enzyme binds both molecules in close proximity
at its active site. The enzyme positions the two molecules in place,
thus decreasing the activation energy required for the chemical
reaction to proceed.
QuickTime™ and a
Photo - JPEG decompressor
are needed to see this picture.
QuickTime™ and a
Photo - JPEG decompressor
are needed to see this picture.
From Biology of Plants p. 80
(P.Raven, R.Evert, S. Eichhorn)
Worth Publishers, New York, 1992
From Introduction to Protein Structure p.206
C. Branden and J. Tooze
Garland Publishing, New York, 1999
Slide 2.2
How does an enzyme function?
Enzymes - Because biochemical molecules come in different sizes,
shapes, with different surface charges (charged, polar, hydrophobic),
then in order for proteins to grab onto them, they must form a
"glove", a pocket at the active site containing the appropriate charges.
It must have a second pocket to grab onto a second molecule.
hydrophobic
+
-
-
Molecule 1 Molecule 2
hydrophobic
-+
+
Enzyme
hydrophobic
+
-
Enzyme + molecules
Change in Protein Conformation
After binding the two substrates, the enzyme may need to change its
shape in order to position them closer together. In addition, the
chemistry may need to be protected from the aqueous environment -for example, a charged molecule may be more attracted to water than to
the second molecule involved in the biochemical reaction. In such a
case, the charged molecule needs to be hidden away from the outside of
the protein into a hydrophobic pocket inside the protein. Because the
binding site of the molecule must be near the surface of the protein, the
binding must cause a change in conformation of the protein such that
the bound molecule is rotated into a cavity inside the protein.
hydrophobic
protective
cavity
charged
H20
Pictures from M. Raizada
H 20
H20
H2 0
Slide 2.3
How do herbicides, pesticides or pharmaceuticals work?:
1. The chemical mimics the real substrate and competes for the
enzyme active site.
Enzyme
+
+
-
-
native
herbicide
substrate
(eg. nitrogen metabolism)
Enzyme-herbicide
binding
2. The chemical binds elsewhere to the enzyme, and because of its
charge, alters the conformation of the enzyme, causing it to be
no longer functional.
Native enzyme
Enzyme + herbicide
In addition, other molecules (phosphate groups, sugars, lipids) can
bind onto proteins and alter its conformation, thus either activating
its function or preventing its function.
Inactive enzyme
Charged phosphate
Activated enzyme
**Hence, small molecules can be used to switch on/off enzymes**.
Source of pictures: M. Raizada
Slide 2.4
How does an enzyme form loops or change its shape?
demo
-Parts of the protein interact with other parts of the protein
(eg. plus to negative, hydrophobic to hydrophobic) to create
loops.
-After substrate binding, the local charge might be
altered, causing the active site to be more attracted to another
internal region of the protein, hence causing a change in protein
conformation.
+
Hydrophobic
stretches
Hydrophobic
stretches
+
+
-
uncharged
region
-
Source of cartoonss:
M. Raizada
*+
Substrate-binding
alters local
protein charge
-
+
+
Positive attracted
to negative,
causes change
in conformation
QuickTime™ and a
Photo - JPEG decompressor
are needed to see this picture.
From Introduction to Protein Structure p.56
C. Branden and J. Tooze
Garland Publishing, New York, 1999
Slide 2.5
Introduction to Amino Acids
To facilitate the binding of molecules and changes in protein
conformation, proteins have an arsenal of 20 amino acid
building-blocks, each with a unique size, shape and charge.
+
P
P
-
H
P
P
P
*
+
H
P
P
P
H
H
H
H
From Biochemistry and Molecular Biology of Plants
(W.Gruissem, B. Buchanan and R.Jones p.360
ASPP, Rockville MD, 2000
H
-
What charges
can amino acids
have?
+ positive charged
- negative
P polar
H hydrophobic
* very flexible
Slide 2.6
Amino acids join together through peptide bonds
that can rotate. Why is this useful?
From An Introduction to Genetic Analysis (6th ed)
A.J. Griffiths et al., page346
W.H. Freeman and Co., New York, 1996
rotate
rotate
Slide 2.7
By placing these at particular places relative to each other in a
3-dimensional chain, they can form the binding sites necessary to
bind molecules for biochemistry or bind one another to form large
structures. Specific amino acids bond to specific regions of the
reactant molecule.
QuickTime™ and a
Photo - JPEG decompressor
are needed to see this picture.
From Introduction to Protein Structure p.60-61
C. Branden and J. Tooze
Garland Publishing, New York, 1999
QuickTime™ and a
Photo - JPEG decompressor
are needed to see this picture.
Slide 2.8
Protein enzymes can adopt multiple shapes by folding.
Protein Folding
To review, what are the molecular functions of an enzyme?
Therefore, why are the shapes of proteins important?
How many different protein shapes (unique folds) are there in all of life?
Is this a surprise?
TIM Barrel - Rubisco
Horsheshow - RNasin
Beta roll - transcription factor Beta barrell - GFP
Slide 2.9
Bonds between amino acids can create elaborate secondary and higher
order scaffolds upon which or within which the biochemistry can be
performed.
alpha-helix
scaffold
From Biochemistry and Molecular Biology of Plants
(W.Gruissem, B. Buchanan and R.Jones) p.347-348
ASPP, Rockville MD, 2000
beta-sheet
scaffold
Alpha/beta
scaffold
structures
create pocket
for enzyme
active site
From Introduction to Protein Structure p.73
C. Branden and J. Tooze
Garland Publishing, New York, 1999
Slide 2.10
Post-Translation
Correct 3-D protein folding: demo
-to create correct enzyme active site and shape
-only <1000 folds in all of life!!!
-DNA is rigid, but amino acid peptide bonds
can rotate, so many combinations
-other protein complexes (chaperones) assist in
folding in a destabilizing aqueous environment
--chaperone
From Biochemistry and Molecular Biology of Plants
(W.Gruissem, B. Buchanan and R.Jones p.438
Slide 2.11
Proteins do not contain the genetic code. Why not??
What features must be possessed by the molecule
selected by evolution to encode the genetic code?
QuickTime™ and a
PNG decompressor
are needed to see this picture.
DNA
RNA
Proteins
What has to be the function of the genetic code?
*Somehow in evolution,DNA “code” had to interact
with amino acids & control how the proteins were
assembled.*
Slide 2.12
Lecture 2 - Key Concepts
1. Because of the variety of amino acids available,
evolution selected proteins to be the main enzymes of life.
2. Enzymes increase the probability that two reactive
molecules will form or break a bond at an active site.
3. Local amino acid charges interact with nucleotides,
other amino acids, chemicals very precisely. Any change
in the local charge or size can cause changes in protein
conformation or binding.
4. The addition or loss of small molecules (phosphates,
lipids, glucose) can be used as an “on/off” switch for
protein activity.
5. Proteins are basically a carbon scaffold upon which
charged or hydrophobic surfaces exist to do biochemistry.
6. Proteins do NOT carry the genetic code, but must
interact with the genetic code.
Slide 2.13