What is Biochemistry

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What is Biochemistry?

• Chemistry and 3-D Structures of Biomolecules
• Molecular Interactions
• Synthesis and Degradation
• Cellular Energetics
• Mechanisms
• Genetics Storage, Transmission, Expression

2
Chapter 1 A Review(What you should remember)

• Origins of Life
• Basic Organic Functional Groups Cpds.
• Components of the Cell
• Basic Terminology
• Thermodynamics
• Essential Equations

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Elements in Living Matter
4

• With the exceptions of oxygen and calcium, the
  biologically most abundant elements are only
  minor constituents of the earths crust.
• Crust
• O 47
• Si 28
• Al 7.9
• Fe 4.5
• Ca 3.5

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Human Composition
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Prebiotic Era 4.6 3.5 billion years ago

• Earths Atmosphere

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Miller and UreyWater Methane Ammonia
Hydrogen
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TERMINOLOGY

• Prebiotic
• Functional Groups
• Condensation Rx
• Hydrolysis
• Polymers

Complementarity Vesicles Compartmentation Natural
Selection Enrichment
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Hydrolysis vs. Condensation Rx

• Both involve water as a product/reactant
• Condensation Rx Water rains out
• Water is formed by the joining of two molecules
  and the splitting out of an H and OH
• Hydrolysis Rx Water is split and is used to
  split or cause lysis of a second molecule
• A molecule is split and water is also split and
  shared as an H and OH to the resulting two
  molecules.

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Functional Groups

• Acyl
• Amido
• Amino
• Carbonyl
• Carboxyl
• Diphosphoryl

Ester Ether Hydroxyl Imino Phosphoryl Pyrophospho
ryl Sulfhydryl
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Elements in Living Matter
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CompartmentationTHINK Membranes
Hydrophobicity

• Vesicles
• Prokaryotes 1 - 10 µm
• Eukaryotes 10 - 100 µm
• Viruses

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Eukaryotic Cell Components

• Eukaryotes
• Organelles
• Endoplasmic Reticulum
• Golgi Apparatus

Mitochondria Chloroplasts Lysosomes Peroxisomes Cy
tosol Cytoskeleton
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Origins of Life

• Evolution
• Creationism
• Intelligent Design
• A critical moment in chemical evolution was the
  transition from randomly generated molecules into
  systems in which molecules were organized and
  specifically replicated.

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How Do Organisms Evolve?

• SYMBIOSIS
• BENEFICIAL MUTATIONS
• ENRICHMENT
• NATURAL SELECTION

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How Do Organisms Evolve?

• Not Directed by the Organism
• Requires Sloppiness
• Constrained by the Past
• Ongoing
• Directed by the Environment

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THERMODYNAMICS(Govern the Spontaneity of
Reactions)

• 1st Law
• The Energy of the Universe (U) is conserved.
• 2nd Law-
• Entropy (disorder) tends to increase.

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THERMODYNAMICS

• 1st Law
• The Energy of the Universe (U) is conserved.
• Energy is neither created nor destroyed.
• Total energy of the Universe (or a system) cannot
  be quantified, but CHANGES within a system often
  can.
• For a single (isolated) system
• ?U (Ufinal UInitial)) q (heat) w (work)

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THERMODYNAMICS

• 1st Law
• The Energy of the Universe (U) is conserved.
• For a single system
• ?U Ufinal UInitial q (heat) w (work)
• Heat random molecular motion
• Work force acting through a distance
• Energy, Heat (Enthalpy), Work
• Joules (J kg m2 s-2) OR Calorie (cal)

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• 1st Law of Thermodynamics -
• The Energy of the Universe (U) is conserved
  thus, for a given system
• ?U ?q (heat) ?w (work)
• For biological systems, most of which are at
  constant pressure,
• 1) work is usually pressure-volume work so w
  P?V
• 2) heat (q) of a system at constant P H
  (enthalpy)
• ? U ? H - P?V
• ? H ? U P?V
• Volume changes are usually insignificant so
• ? H ? ? U

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Spontaneity of a Rx
Enthalpy measures alone will not determine the
spontaneity of a Rx
Can heat (enthalpy) force all the molecules back
into one side?
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THERMODYNAMICS

• 2nd Law-
• Entropy (disorder, randomness) tends to increase.
• Chemicals like to exist in disordered arrays and
  will naturally progress to a less ordered state
  when no energy is added.
• Spontaneous Rxs USUALLY result in reactants in a
  less ordered state.

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Spontaneity of a Rx
Enthalpy alone cannot determine the direction of
a Rx
Heat
because Entropy favors the less ordered state.
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THERMODYNAMICS

• 2nd Law - Entropy tends to increase and we can
  estimate entropy by
• Entropy (S) kB ln W
• (S Joules per degrees Kelvin or J K-1)
• Where
• W energetically equivalent ways
• kB Boltzmans Constant 1.4 x 10-24 J K-1

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THERMODYNAMICS

• 2nd Law- Entropy tends increase, and
• Entropy (S) kB ln W
• The most probable or favored arrangement of a
  system is one that maximizes W and, hence,
  maximizes S.
• Thus, the W in the final state must be greater
  than the W of the initial state.

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• 2nd Law- Entropy tends increase, and
• Entropy (S) kB ln W
• We cannot determine W for biological systems,
• but in a closed system at constant T and P
• (remembering the unit of S are JK-1)
• q/T ? ?S
• (the heat of the system divided by the
  temperature of the system gives the units of
  S),
• and q ?H for biological systems, so
• ? H/T ? ?S

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THERMODYNAMICS

• ? H/T ? ?S
• Or
• (true criterion for spontaneity by J. Willard
  Gibbs)
• H - T ?S ? 0
• G ? H - T ? S
• If ?G is negative spontaneous (exergonic)
• If ?G is positive NOT spontaneous (endergonic)

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Spontaneity Chart(searching for negative ?G)
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State FunctionsFree Energy, Energy, Enthalpy,
Entropy

• These functions depend only of beginning and end
  states. Stepwise changes must still result in
  the same final values
• Example Combustion of glucose. The same
  energy change occurs by combustion to CO2 and H2O
  as occurs with multiple enzymatic steps in a
  cell.

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State FunctionsFree Energy, Energy, Enthalpy,
Entropy

• Concentration Dependant
• entropy (and, hence, free energy) increases
  with volume hence, we are concerned with the
  partial molar free energy

GA-GºA RT lnA
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State FunctionsFree Energy, Energy, Enthalpy,
Entropy

• Temperature Dependant
• vant Hoff plot allows calculations of ?Hº,
  ?Sº, and ?Gº by measuring Keq at two or more
  temperatures.
• ?G RT ln Keq
• ln Keq ?Hº x 1 ?Sº
• R T
  R

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Standard State Conventionsfor Biochemistry

• Most Rxs are in an aqueous environment hence,
  pH becomes a factor.
• Pure water is 55.5 M, but it is assigned an
  activity of 1 at Standard State.
• At pH 7.0, H 10-7 M
• (this is SS not pH 0)
• The total concentration of a substance capable of
  acid-base reaction is defined in terms of total
  at pH 7
• ( not of specific ionic species and not at pH0)

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Standard State Conventionsfor Biochemistry

• Thus, remember
• ?Gº ' is more defined than ?Gº,
• which is more defined than ?G
• ?Gº -- 298 ºK 1 atm solutes 1 M
• ?Gº -- pH 7.0 H20 55.5 M and H 10 7
  M

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Standard State Conventionsfor Biochemistry

• Thus, remember
• ?Gº ? ?Gº '
• If the Rx includes H20, H, or an ionizable
  species
• And
• ?Gº ' means that the activity of water and
  hydrogen ion activity are arbitrarily assigned a
  value of 1.

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Does Life Obey the Laws of Thermodynamics?

• Life persists because a system can be ordered at
  the expense of disordering its surroundings

• Living organizisms are open systems they are not
  at equilibrium

• Nature is inherently dissipative efficiency is
  always less than 100

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ENZYMES

• Enzymes accelerate biochemical Rxs by physically
  interacting with the reactants and products to
  provide a more favorable pathway .
• Enzymes (like catalysts) may increase the RATE of
  a Rx.
• Enzymes May NOT promote Rxs with positive ?Gs.