Biochemistry 3511, Lectures 1-2
Introduction
• Chem 4511 or 6501 students: your class is in Boggs 6A
• Purpose of the class: - to allow you to understand how important life processes work by reasoning from a set of principles and recognized patterns
- to give you a basic biochemistry vocabulary - to provide examples of how living systems generate and manage molecular information
- to give you an appreciation for just how cool the chemistry of life is
• Disclaimer: we can only discuss a very limited number of examples of each
idea; lots of exceptions, extensions, and consequences will be left out. I’m sorry
about this. For you to do
• familiarize yourself with T-square
• sign up for Sapling Learning and Piazza (see syllabus for instructions)
• get the textbook and read Chapters 1-2
• look over the syllabus and get ahead on your reading for upcoming weeks
• start looking at end-of-chapter problems in the book and those on Sapling
• start putting together your video team
your instructors
Ms. Saira Dar
- School of Chemistry & Biochemistry
- second-year graduate student, co-advised by Profs. Donald Doyle and M.G. Finn
- Research project: manipulation of human nuclear receptors in yeast to assist the production of desired compounds by biosynthetic routes.
- “I am happy to be your TA for this semester. You are more than welcome to consult me with any problem and I am open to any good suggestions you might have.”
your instructors
Ms. Saira Dar
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2012-current - Biochemistry Graduate student
in School of Chemistry and Biochemistry at
Georgia Institute of Technology
2010- 2011 - Research Assistant in School of
Science and Engineering at Lahore University of
Management Sciences, Pakistan
2008-2010 – Masters in Molecular Biology,
University of the Punjab, Pakistan 2007-2008 - Research Student in Basic Science
Research Lab in Shaukat Khanum Memorial
Hospital and Research Center, Lahore, Pakistan
2006 - Intern in Institute of Nuclear Medicine
and Oncology (INMOL), Lahore, Pakistan
2003-2007 –Bachelors Degree in Biochemistry
from University of the Punjab, Pakistan
your instructors
Mr. Michael Rood
- School of Chemical and Biomolecular Engineering
- fifth-year graduate student, advised by Prof. Andy Bommarius
B.S., Chemistry
2006
Toledo, OH
Using Nuclear Receptors for
Enzyme Engineering
Engineered Enzyme Discovery for Drug Production: Increase yield/
productivity; lowered waste/emissions
High-Throughput Enzyme Library Analysis
your instructors
M.G. Finn, Ph.D.
- Schools of Chemistry & Biochemistry and Biology
- grew up in New Jersey, but roots in New England, so my household is
a Red Sox-and-Celtics zone
-  undergraduate at Caltech (inorganic chemistry), Ph.D. at MIT (inorganic and
organic chemistry), postdoc at Stanford (organometallic chemistry)
-  professor at University of Virginia (1988-1998); moved to The Scripps
Research Institute (1999-2013), then to Georgia Tech in March
-  wife (Beth) is a math teacher; two children, neither of whom do math or
science
-  hobbies are music (jazz and salsa), cooking, and basketball
Finn Group research: Engineered Virus-­‐Like Particles • genetically and chemically tailorable
nanoparticles
• precise control of structure and function
• cell targeting units on the outside;
dyes, drugs, contrast agents, catalysts inside
• confer immunogenicity to attached molecules
New Targets and Opportunities
• new particles
• catalytic pathways inside and outside
• evolved particles for advanced capabilities
• cancer targeting for diagnostics and therapy
• glycan-based and slow-release vaccines
• therapeutic enzyme replacement
Cell Targeting with Functionalized Particles A-­‐431 cells HT-29 cells
Qß(EGF)7
@(AF488)20
Zina Polonskaya, Marisa Hovlid, Jon Pokorski
Medicinal Chemistry Targets
Methods
• Small-molecule agents against proteins of
medical importance:
- HIV
- hepatitis B virus (HBV)
- GABAB receptor (nicotine addiction) • traditional heterocyclic, carbohydrate, and other small-molecule synthetic methods
- Protein arginine methyl transferases (PRMTs)
• target-guided, in situ click chemistry: allowing the protein to make its own ligands Analytical chemistry: a general approach to detecting binding interaction of any two species changes: hydration dipole moment ionic strength number of particles cohesive energy density other stuff backscattering interferometry Label-free, solution-based measurement.
Large range detectable (pM–µM affinities)
Small volumes (1-10 µL)
Avg. detection limit ≈50 pM
What we use it for:
- membrane-bound protein targets
- things inside viruses
- correlate enzyme inhibition with
binding
Biochemistry deals with the chemistry of living matter
Life is characterized by
• 
A high degree of complexity • 
Extraction, transformation, and systematic use of energy to
create and maintain structures and to do work
• 
The ability to sense and respond to changes in surroundings
• 
A capacity for fairly precise self-replication while allowing
enough change for evolution Some overall points:
•  Life derives from and harvests energy gradients: living systems
are not at equilibrium!
•  Self-replication and compartmentalization à mutation à
evolution
•  Look for units of function: we’ll be going from the atomic to the
organismal, but biology is able to propagate complex functions as
easily as simple ones
Life derives from and harvests energy gradients
Life derives from and harvests energy gradients
Eric D. Schneider & Dorion Sagan
Erwin Schrödinger
Born August 12, 1887
Life derives from and harvests energy gradients From “Into the Cool”
“In 1943 Nobel Laureate Erin Schrödinger…gave a series of three
lectures at Trinity College in Dublin. While not a biologist, his
lectures were titled "What is Life: The Physical Aspect of the Living
Cell". In 1944 he published these lectures in a 91-page book by the
same title. This ground breaking work saw two processes in biology. One he
termed "order from order” … [suggesting] how the genetic program
is passed from parent to progeny. His final lecture focused on what he called "order form disorder"; he
asked the question on how living systems made prodigious order
from disordered molecules and atoms when the second law of
thermodynamics suggested such systems should be falling apart
over time.”
The answer? Life isn’t a closed system! It steals energy from the environment, managing its use in stages to achieve self-­‐sustaining and self-­‐replicating systems. This demands staged storage and use of energy, spatial barriers, Eric D. Schneider & Dorion Sagan
and increased information content. It Living systems extract energy
•  From sunlight
–  plants
–  green bacteria
–  cyanobacteria
•  From fuels
–  animals
–  most bacteria
•  Energy input is needed in order to
maintain complex structures and be in a
dynamic (steady) state, away from
equilibrium
Chapter 1
Introduction to the Chemistry of Life
Key Concepts • Biological molecules are constructed from a limited number of elements. • Certain func:onal groups and linkages characterize different types of biomolecules. • During chemical evolu:on, simple compounds condensed to form more complex molecules and polymers. • Self-­‐replica:ng molecules would have been subject to natural selec:on. • Self-­‐replica:on and compartmentaliza:on à muta:on à evolu:on • Look for units of func*on: we’ll be going from the atomic to the organismal, but biology is able to propagate complex func:ons as easily as simple ones • We’ll look at the chemistry behind: -­‐ accelera:ng reac:ons (controlling when something happens) -­‐ building compartments and micro-­‐environments (controlling where something happens) -­‐ storage and transfer of informa:on How we talk about energy
“Thermodynamics” is presented as the study of energy and its effect on maNer. We will use this term more specifically: Thermodynamics refers to the energe:cs of a process (usually a chemical reac:on) at equilibrium. Kine0cs refers to the speed (rate) at which a chemical process occurs. -­‐  Let’s discuss: simple equilibria -­‐  Free energy: G = H – TS (H = enthalpy, T = entropy) -­‐  Change in these parameters (ΔG = ΔH – TΔS) defines the overall energy change in going from reactants to products. **Don’t focus on text discussions of laws of thermodynamics.
**Text discusses free energy in terms of reaction “spontaneity.” This is not
accurate, as we shall see… How we talk about energy
An important class of reac:ons is simple binding, and we’ll see lots of it: A
kon
B
+
koff
A B
Keq =
[A-B]
[A][B]
=
kon
koff
Reac:ons in which bonds are made and broken are governed by the same parameters: N
N
O O O O O O
P
P
P
HO
O
O
O
O
N
N
N
NH2
N
+ H2O
solvent (pH 7)
HO
OH
ATP
(adenosine triphosphate)
1 M (start)
O O O O
P
P
HO
O
O
O
HO
N
NH2
N
OH
ADP
(adenosine diphosphate)
ΔG0 = -7.3 kcal/mol = -30.5 kJ/mol
+
O O
P
HO
OH
How we talk about energy
Entropy increases: it costs energy to fight this!
How we talk about energy
ΔG0 = –RT ln Keq R = gas constant (1.987 kcal/mol) Keq = equilibrium constant (concentra:ons of products / concentra:ons of reactants) ΔG0 = –RT ln Keq Keq
B
A
How we talk about energy
How much energy are bonds worth? Covalent bonds:
homoly:c bond dissocia:on energies in units of kcal/mol (essen:ally, this is enthalpy) Larger values = “more stable” bonds, Implying lower reac:vity
Don’t memorize these numbers.
How we talk about energy
N
N
O O O O O O
P
P
P
HO
O
O
O
O
HO
N
N
N
NH2
N
+
H
O
H
H
O O O O
P
P
O
O
O
OH
O
HO
N
NH2
N
+
O O
P
HO
OH
OH
ΔG0 = -7.3 kcal/mol = -30.5 kJ/mol
ΔG = ΔH – TΔS
• Going from one species to two is worth roughly 10 entropy units (cal / mol °K) • at 295 °K, 10 eu is worth 2.95 kcal/mol but, consider ATP: life’s energy currency
N
N
NH2
N
O O O O O O
P
P
P
HO
O
O
O
O
N
HO
+
N
NH2
N
H
O
H
O O O O
H
P
P
O
O
O
OH
O
HO
N
N
N
N
O O O O
P
P
HO
O
O
O
HO
N
N
NH2
N
+ H2O
HO
O O
P
O
O
HO
OH
ADP
(adenosine diphosphate)
O O
P
HO
OH
inorganic
pyrophosphate
OH
ΔG0 = -7.3 kcal/mol = -30.5 kJ/mol
N
+
N
NH2
N
OH
AMP
(adenosine monophosphate)
ΔG0 = -8.5 kcal/mol
+
O O
P
HO
OH
How can reactions be speeded up?
Higher temperatures Stability of macromolecules is limi:ng Higher concentra:on of reactants Costly as more valuable star:ng material is needed Change the reac:on by coupling to a fast one Universally used by living organisms Lower ac:va:on barrier by catalysis Universally used by living organisms Unfavorable and favorable reactions
•  Synthesis of complex molecules and many other metabolic reac:ons requires energy (endergonic) –  A reac:on might be thermodynamically unfavorable (ΔG° > 0) •  Crea:ng order requires work and energy ‡
–  Metabolic reac:on might have too high energy barrier (ΔG > 0) •  Metabolite is kine:cally stable •  Breakdown of some metabolites releases significant amount of energy (exergonic) –  Such metabolites (ATP, NADH, NADPH) can be synthesized using the energy from sunlight and fuels –  Their cellular concentra:on is far higher than their equilibrium concentra:on. Reaction coordinate diagrams
Catalysis
•  A catalyst is a compound that increases the rate of a chemical reac:on ‡
•  Catalysts lower the ac:va:on free energy ΔG •  Catalysts does not alter ΔG° •  Catalysis offers: –  Accelera:on under mild condi:ons –  High specificity –  Possibility for regula:on Chapter 1
**Book error: page 19, “Living Things Maintain a Steady State”
“This means that all flows in the system are constant so that the system does not change with time…”
Now let’s start with the building blocks… • Key proper:es: valence, electronega:vity, type of bonds formed Living matter consists mainly of only a few elements
Functional groups: the units of chemical….uh…function
Func:onal groups common to biological molecules: acids and bases (carboxylic acids and amines) connectors (amides, esters, phosphates, disulfides, ethers) electrophiles (aldehydes, ketones, esters, imines, phosphates) nucleophiles (thiols, amines, alcohols, water) things that interact with water (alcohols, and some of the above) rings and heterocycles Functional groups: the units of chemical….uh…function
Func:onal groups common to biological molecules: acids and bases (carboxylic acids and amines) connectors (amides, esters, phosphates, disulfides, ethers) electrophiles (aldehydes, ketones, esters, imines, phosphates) nucleophiles (thiols, amines, alcohols, water) things that interact with water (alcohols, and some of the above) rings and heterocycles Functional groups: the units of chemical….uh…function
Func:onal groups common to biological molecules: acids and bases (carboxylic acids and amines) connectors (amides, esters, phosphates, disulfides, ethers) electrophiles (aldehydes, ketones, esters, imines, phosphates) nucleophiles (thiols, amines, alcohols, water) things that interact with water (alcohols, and some of the above) rings and heterocycles What they do is mostly bind to each other and make/break bonds
explore zinc finger binding to DNA …which makes this
possible