PHS 2201- Chapter 1

Central Dogma of Biochemistry

1) Inherited information can be stored in cells and transferred to offspring using biological molecules/changes in the stored information can be altered to introduce variability within species but also cause disease.

2) Provide the structure by which cells and organisms are built.

3) Carry out functions important for life.

mRNA —> DNA —> Protein

Spontaneous Generation

Living organisms arise from nothingness.

1860’s – Demonstrated that bacteria exist in air (Louis Pasteur)

Led to Cell Theory

Vitalism

Living systems do not obey the same chemical principles as inert materials

Challenged by Wohler in 1828 with discovery that urea can be synthesized from ammonia and bicarbonate.

In 1897 Eduard and Hans Buchner demonstrated fermentation could exist in an extract from ruptured cells.

Collision Theory

Rate of reaction is proportional to the number of collisions

Concentration of reactant directly proportional to collision chance.

Forward Reaction Rates

Rate of substrates conversion to products

A + B → C + D

rate_f = k_f [A][B]

Reverse Reaction Rates

Rate of products returning to substrates

C + D → A + B

rate_r = k_r [C][D]

Rate Constant

Forward Rate = k_f

Reverse Rate = k_r

Constant of proportionality between rate and concentration.

Equilibrium

Forward and reverse reactions equal each other

rate_f = rate_r

k_f [A][B] = k_r [C][D]

k_f / k_r = [C][D] / [A][B] = K_eq

While a single reaction may exist in equilibrium, so may multiple reactions.

Relates kinetics (rate process tied to a time element) to equilibrium (independent of time)

The Steady State

Living cells are never actually at equilibrium

Need substrate (S), intermediate (I), and product (P)

S → I → P

S → I → J → K →L → P: Can be better suited to describe what looks to be equilibrium

Thermodynamics (Classical Approach)

Few postulates and definitions

Makes no assumptions about the exact nature of the systems under investigation

Description of the system at near-equilibrium, using properties which are measurable

Consistent set of equations

Thermodynamics (Statistical Approach)

Considers behavior of large collections of molecules

Allows for more mechanistic conclusions

More narrowly applicable

Consistent set of equations

Internal Energy

Energy of the system under study

Sum of the work (energy of motion) and heat of the system

Enthalpy

Heat released or absorbed by a reaction

Entropy

Number of ways energy can be distributed

Increases with an increase in energy dispersion

Free Energy

Combination of enthalpy and energy

Used to determine if a reaction will proceed

∆G = ∆H - T∆S

NADH

Nicotinamide adenine dinucleotide

High energy electrons

ATP

Adenosine triphosphate

High energy phosphate

Cellular Currency

Cell Theory

Cells are the fundamental unit of living systems

Smallest unit of life

Single Cell Organisms vs. Mammalian Cells

Single Cell: Largest number of species/prokaryotes (i.e., bacteria, yeasts, protozoans)

Mammalian: Multicellular organisms

Internal organelles (mitochondria, endoplasmic reticulum, nuclear membrane)

Semipermeable membrane (plasma membrane)

Create separate water spaces to isolate chemical reactions

Need to communicate across these spaces, diffuse, or utilize a specific transporter to cross membrane

Evolution

Charles Darwin’s work in the Galapagos Islands of Ecuador “On the Origin of Species”

Species arose from other species

Those that could adapt best to their environment were able to survive because they lived to reproduce.

Adaptive Characteristics

Traits that best survive a condition stay, those that do not, die out.

Evolution in Biochemistry

Map the formation of enzymes and DNA sequences

Numerous enzymes and DNA sequences diverge from their origin

Classical Hierarchy

Organize the diversity of life

Catalog the complexity of the immense number of known species

3 of 5 kingdoms studied in biochemistry:

Animals – Plants – Prokaryotes

Biological Systems (Holistic View)

View close to top

Widest view possible

Answers questions that are physiologically relevant

Biological Systems (Reductionist View)

Molecular view

Molecular interactions