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BCHS 3304 General Biochemistry (13830) Monday/Wednesday 2:30-4:00pm, SW102

Course Homepage on Blackboard (Slides, Notes, Syllabus, etc.)

Steven J. Bark, Ph.D.

The Scripps Research Institute

Mass Spectrometry, Protein Chemistry, Biochemistry

Office: 4022 SERC

Office Hours: Monday/Tuesday 1-2pm or by appointment

Communications: Office 713-743-9638, Blackboard, sbark@uh.edu

Blackboard or email is the best way to reach me!

Sian Behrendt-McLeroy

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4 Exams and a Comprehensive Final (See Syllabus)

Good performance on the FINAL EXAM will replace poorer

performance on ONE earlier exam

Exams based on Lectures, Textbook, Study Guide, Problems

You MUST take ALL exams. NO exams are dropped. There are NO

makeups. There is NO extra credit.

This is not an Easy A Course!

You SHOULD attend every lecture! You SHOULD work through every

problem in the textbook and study guide!

You are responsible for all information!

Group homework and study sections is encouraged, but copying the

homework and not fully participating = disaster!

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I AM ON YOUR SIDE AND WILL DO WHAT I CAN TO

GUARANTEE YOUR SUCCESS IN THIS COURSE,

BUT I CANT DO IT FOR YOU!!!

BIOCHEMISTRY IS COMPLEX AND FAMILIARITY IS NOT

ENOUGH!

READ! STUDY! QUESTION! ORGANIZE! UNDERSTAND!

LEARNING IS AN ADVENTURE! HAVE FUN!

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Chapter 1: Intro to the Chemistry of Life

Biochemistry is the study of the chemistry of life. Biochemistry is an interdisciplinary science overlapping with chemistry,

cell biology, genetics, immunology, microbiology, pharmacology, and

physiology.

Primary Questions in Biochemistry

1. Chemical and three-dimensional structures of biological molecules?

2. How do biological molecules interact with each other?

3. How does the cell synthesize and degrade biological molecules?

4. How is energy conserved and used by the cell?

5. What are the mechanisms for organizing biological molecules and

the coordinating of their activities?

6. How is genetic information stored, transmitted, and expressed?

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The physical laws of the universe apply to living organisms:

Laws of conservation of mass, energy

Laws of thermodynamics

Laws of chemical kinetics

Principles of chemical reactions

In practical terms, living organisms:

Assemble molecules with great complexity from simple subunits. Combine these molecules to form organized supra molecular

components, organelles and finally assemble into a cell.

Replicate, store, and pass on information for the assembly of future generations from simple non-living precursors

Convert energy to work Employ catalytic chemical transformations

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Prebiotic World

~4.6-3.5 billion years ago Earliest known fossil is ca. 3.5 billion

years old (filamentous bacterium).

Most organisms are ca. 70% water

Living matter consists of a small number

of elements

Elemental composition of the human

body (97%)

Trace: B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni,

Cu, Zn, As, Se, Br, Mo, Cd, I

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Prebiotic World No direct fossil record of prebiotic conditions!

Possible early atmosphere consisted of H2O, N2, CO2,

small amounts of CH4, NH3

Sparking of a mixture of CH4, NH3, H2O, and H2 for 1

week yielded (Stanley Miller and Harold Urey)

Acids (formic, glycolic, lactic, propionic, acetic,

succinic, aspartic, glutamic, etc.)

Amino acids (glycine, alanine, aspartic, glutamic)

Others (urea, sarcosine, N-methyl-alanine, N-methyl-

urea, etc.)

Some scientists propose that early biological

molecules were created in the dark underwater at

hydrothermal vents, thermophile bacteria

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IMPORTANT! charge state of some functional groups differ in different environments/conditions (e.g., COOH and COO-; NH3 and NH4+)

Key Organic Functional Groups

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Key Organic Functional Groups. cont

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Chemical Evolution

Many enzymes catalyze hydrolysis and condensation reactions

Hydrolysis = water breaking

Condensation = assemble together

In particular, the condensation reaction has been very useful throughout evolution for increasing biological complexity

Of course, the hydrolysis carries out the reverse reaction, leading to a loss in biological complexity

Complementarity enables replication

through templating (e.g., COO-NH4+)

Base complementarity in DNA

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Compartmentation = sequestering into a compartment (vesicle)

Vesicles (fluid-filled sacs) are thought to be the precursors to cells

These entities would have had the ability to shield self-replicating chemical reactions and catalyzed reactions so that they were taking place in a sheltered environment, higher concentration of nutrients and ions, giving them a competitive advantage

Catalyst is a substance that promotes a chemical reaction.

This compartment then has the opportunity to further evolve in order to enhance its advantage.

A typical animal cell contains as many as 100,000 different types of molecules

A common bacterium, E. coli, contains millions of molecules, representing 3000-6000 different compounds.

Cellular Architecture

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All modern organisms are based on the same morphological unit, the

cell

Prokaryotes lack a nucleus (e.g., bacteria, archaea): 1 to 10 mM

Eukaryotes membrane enclosed nucleus encapsulating their DNA

(e.g., animals, plants, fungi): 10 to 100 mM

Viruses are not cells and are not defined as living since they lack the

apparatus to reproduce outside of their host cells.

Eukaryote compartmentation extends to other cellular structures: Endoplasmic Reticulum, Mitochondria, Golgi Apparatus, Lysosomes, etc.

Prokaryotes and Eukaryotes

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Taxonomy:

biological

classification

Phylogeny:

evolutionary

history

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Evolution

1. All organisms change over time to adapt to changes in their

environment.

This is an observation, not a theory.

2. On the Origin of Species (1859) by Charles Darwin articulated a

that evolutionary processes could occur by natural selection.

Natural selection is a theory, but has been subjected to

experimental observations and experiments.

3. Evolution occurs over short and enormously long time scales.

Adaptations occur within single members of a population (one

lifetime), but are continuous from the dawn of life (>3.5 billion

years ago) to the end of life (~2 billion years from now) on Earth.

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Principles of Evolution

1. Evolution is not directed toward a particular goal.

It proceeds via random changes called mutations. Organisms that

are better suited to reproduce in their environment flourish.

2. Evolution requires some built-in sloppiness.

This is the source of mutation. It allows for adjustment to

unforeseen changes in the environment.

3. Evolution is constrained by its past.

The new arises from the old.

4. Evolution is ongoing.

Not always toward increasing complexity.

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Size Matters! Length Scale for Life Smaller Larger Diffraction Methods (X-ray, EM, AFM, 0.2um)

1 10 100 1000 104 105 106 107 10-10m 10-9m(1nm) 10-8m 10-7m 10-6m(1mm) 10-5m 10-4m 10-3m

C-C bond (1.54)

Hemoglobin (65)

Ribosome (300)

Virus (100-1000)

Prokaryote Cell

(10k-100k, 1-10um))

Eukaryotic Cell

(100k-1000k, 10-100um)

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Time Matters! Life is Very Dynamic

10-15 s 10-12 s 10-9 s 10-8 s 10-6 s 10-3 s 10 s 103s

femto pico nano micro milli sec

Reference Time Scales:

femto, fs excitation of chlorophyll

pico, ps charge separation in photosynthesis

nano, ns hinge protein action

10-8 (10 ns) fluorescence lifetime

micro, ms DNA unwind

milli, ms enzymatic reactions

103 s generation of bacteria

2.3 x 109 s average human life span

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Energy Matters! Life Uses Energy

Ultimate Energy Source = Stellar Fusion (Sun)

E = hn =57 kcal/mol of photons green light or 238.k kJ/mol

1 kcal = 4.184 kJoules

0.239 kcal = 1 kJ

ATP ADP + Pi = -7.3 kcal/mol or -30.5 kJ/mol

IR Energy (vibrational) = 0.6 kcal/mol or 2.5 kJ/mol

C - C bond = 83 kcal/mol or 348 kJ/mol

Ionic interactions ~86kJ/mol

van der Waals interactions < 20kJ/mol

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Thermodynamics First Law Energy (U) is conserved it can be neither created

nor destroyed

The Enthalpy (H) of a process is defined as follows:

H = U + PV

Absolute measures of state functions can be very difficult to

obtain. Fortunately, most often interested in changes (D)

DH = DU + PDV (under constant pressure, the volume will change like the expansion of a gas)

Under biological conditions, pressure is constant and the

volume changes are practically negligible:

DH DU

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Thermodynamics Second Law

Spontaneous processes are characterized by the

conversion of order to disorder, increased entropy (S).

A process is spontaneous if it can occur without the input of

additional energy from the outside of the system

Entropy (S) is the measure of the degree of disorder in a system, often

related to the number of states a system can adopt.

In the system to the right, the top

system is more ordered than the

bottom.

The entropy increases on going from

the top to the bottom system.

The change in entropy is measured

by: DS = DH/T (T=temperature)

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Gibbs Free Energy (G)

The Gibbs Free Energy (G) change of a

spontaneous process is negative, DG < 0

Free energy is defined as follows: G = H TS

Normally, we are interested in the change in free

energy so the following equation is more useful:

DG = DH TDS

If the DG is < 0, the process is called exergonic

If the DG is > 0, the process is called endergonic

If the DG is = 0, the process is called equilibrium

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Equilibrium Constants Relationships between free energy of a system and

concentration of reactants and products at a particular state

DG0 = free energy change in the equilibrium state

At equilibrium, DG=0 so DG0 = -RT ln Keq

R (gas constant) = 8.3145 J/K-mol

RTG

beq

aeq

deq

ceq

eq eBA

DCK /0

][][

][][D

DD

ba

dc

BA

DCRTGG

][][

][][ln0

dDcCbBaA

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Equilibrium Constants Equilibrium constant varies with temperature. At

equilibrium:

DGo = DH

o TDS

o

DGo = -RT ln(Keq)

Substitution and algebraic rearrangement:

ln(Keq) = - DHo 1 + DS

o

R T R

Measurement of Keq at two different temperatures enables calculation of DH

o and DS

o directly.

vant Hoff

Equation

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Biochemical processes operate in a forward

manner as long as the overall pathway is

exergonic! Have to consider all steps!

Coupling ATP hydrolysis (highly exergonic

reaction) to drive many otherwise endergonic

biological processes to completion!!

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Standard state conventions in

biochemistry The activity of pure water is assigned a

value of 1 even though it concentration is

really 55.5 M (M = Molar). Therefore, the

terms for the concentration of water, [H2O],

in equilibrium expressions can be ignored.

The standard pH is 7.0 (10-7 M)

Temperature is 25oC (298K)

Pressure is 1 atm (atmosphere)

Standard concentration is 1M

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For next time

Read Chapter 2, Section 1- We will cover most

of it next time in class.

Work as many problems in Chapter 1 Textbook

and Student Companion as you can.