Biochemistry CHAPTER 1

CHAPTER 1 Foundations of Biochemistry

Brief History of Biochemistry Physical Science
Learning Objectives (Chemistry, Physics) Biological Science
 Distinguishing features of living organisms *Biochemistry came on the science scene in the early 1900s with the appearance of
 Structure and function of cells and organelles the first biochemical journals, the formation of a section of biological chemistry by
the American Chemical Society, and the creation of biochemistry departments in
 Roles of small and large biomolecules research universities and medical schools.
 Energy transformation in living organisms The branch of science dealing with the study of all the life processes such as control
 Regulation of metabolism and catalysis and coordination within a living organism is called Biochemistry. This term was
 Coding of genetic information in DNA introduced to us by Carl Neuberg, the father of biochemistry in the year 1930.
 Mutation, selection and evolution
 Molecular phylogeny Biochemistry- Molecular Biology
The term molecular biology was first coined in 1938 by Rockefeller
Fundamentals of Biochemistry Foundation Biochemistry and molecular biology have similar goals;
“life’s processes at the level of molecules” however, their approaches to solving problems have been different in the
past:
What is Biochemistry? Molecular biologists– emphasize the study of genetic materials
In this course you will be introduced more complex but exciting concepts in (RNA and DNA), especially its role in biological information
Biochemistry transfer and they use more biological experimental approaches
Biochemists use basic laws of involving organisms, recombinant DNA and molecular genetics
Chemistry, Biology and Physics to explain? Processes of living Biochemists– focus on the structure and function of all
cells biomolecules and energy relationships among them.

Even though the word Biochemistry has become common place in  In fact, most scientists consider the fields to be the same.
our language, a concise meaningful definition is difficult  Both becoming indistinguishable because they seek answers to the
same question: what is life?
Simplest definition is: “The chemistry of the living cell”
Overall goal of biochemistry is to describe: “life’s processes at the Cells: Universal Building Blocks
level of molecules” Living organisms are made of cells
Simplest living organisms are singe-celled
All biological processes including vision, digestion, thinking, Larger organisms consists many cells with different functions
motion, immunity and disease conditions result from the actions of Not all the cells are the same
molecules
Three Domains of Life
Therefore, in order to describe these processes …? One must have a Differences in cellular and molecular level define three distinct domains of
life
I. Knowledge of chemical structures of participating molecules
(Conformational study)
II. Understanding of the biological function of cellular molecules
(Informational)
III. Study of energy flow is living system ---- (Bioenergetics)
Biochemistry CHAPTER 1

-Spatial separation of energy-yielding and energy consuming

Bacterial, Plant, and Animal Cells are Different reactions helps cells to maintain homeostasis and stay away from
The internal structure and properties of cells from organisms in different equilibrium
kingdoms are rather different but fundamental macromolecules are highly
conserved Components of Animal Cells

Components of Bacterial Cell

Structure Composition Function Chemical Composition of Cell
Cell wall Peptidoglycan Mechanical support
Cell membrane Lipid + protein Permeability barrier
Nucleoid DNA + protein Genetic information
Ribosomes RNA + protein Protein synthesis
Pili Protein Adhesion, conjugation
Flagella Protein Motility
Cytoplasm Aqueous solution Site of metabolism

Eukaryote Cells: More Complexity

-Have nucleus by definition
 protection for DNA; site of DNA metabolism
 selective import and export via nuclear membrane pores
 some cells become anuclear (red blood cells)
-Have membrane-enclosed organelles
 Mitochondria for energy in animals, plants and fungi
 Chloroplasts for energy in plant
 Lysosome for digestion of un-needed molecules
Biochemistry CHAPTER 1

Cytoplasm and Cytoskeleton

Cytoplasm is highly viscous solution where many reactions take Energy and Carbon Sources
place All organisms require energy and carbon for life We can also classify based
Cytoskeleton consists of microtubules, actin filaments, and in the sources of energy and carbon
intermediate filaments cell shape transport paths movement

Structural hierarchy in the molecular organization of cells. The nucleus of

this plant cell is an organelle containing several types of supramolecular
complexes, including chromatin. Chromatin consists of two types of
macromolecules, DNA and many different proteins, each made up of simple
subunits.

Elements of life Elements

H, O, N, P, S are also common
Metal ions (e.g. K+, Na+, Ca++, Mg++, Zn++, Fe++) play
important roles in metabolism
Together, about 30 elements are essential for life

Living Systems Extract Energy

-From sunlight
 plants Elemental composition of Life: Unique Role of Carbon
 green bacteria Biomolecules are carbon-based
 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 the equilibrium
Biochemistry CHAPTER 1

Biological Molecules Typically Have Several Functional Groups Optical Isomers have Different Biological Properties
Enantiomers have identical physical properties (except regard to
polarized light) and react identically with achiral reagents.
Diastereomers have different physical and chemical

Interactions between Biomolecules are Specific

Macromolecules have unique binding pockets
Structure of Biological Molecules is Important
Only certain molecules fit in well and can bind
The function of molecules strongly depend on three-dimensional structure
Binding of chiral biomolecules is stereospecific

Thermodynamics - Energetic Driving Forces

 G = H – TS
 Free Energy = Enthalpy – (T × Entropy)
 Spontaneous Chemical Processes are characterized by reduction in
Free Energy
 Reactants => Products
 GProducts – GReactants = ΔG = ΔH – TΔS
 Spontaneous if ΔG is negative

Free Energy
Stereoisomers have Different Biological Properties  Every Chemical Compound has a standard Free Energy of
Cis and trans isomers have also different physical and chemical properties Formation G°
 The standard state is typically 1 M, 25°C
 For biochemical reactions pH (7.0) is specified as well
 The conversion of 1 mole of:
 A + B => C + D
 ΔG° = (G°C + G°D ) - (G°A + G°B )
Biochemistry CHAPTER 1

Chemical Equilibrium

Unfavorable and Favorable Reactions

Synthesis of complex molecules and many other metabolic reactions
requires energy (endergonic)
 A reaction might be thermodynamically unfavorable (G° > 0)
Creating order requires work and energy
Breakdown of some metabolites releases significant amount of energy Energy Coupling
(exergonic) Chemical coupling of exergonic and endergonic reactions allows
 Such metabolites (ATP, NADH, NADPH) can be synthesizes otherwise unfavorable reaction
using the energy from sunlight and fuels The “high-energy” molecule (ATP) reacts directly with the
 Their cellular concentration is far higher than their equilibrium metabolite that needs “activation”
concentration.

ATP: Chemical Currency of Energy

Kinetics – Reaction Rate Acceleration

Higher temperatures
-Stability of macromolecules is limiting

Higher concentration of reactants

-Costly as more valuable starting material is needed
Biochemistry CHAPTER 1

Change the reaction by coupling to a fast one

-Universally used by living organisms

Lower activation barrier by catalysis

-Universally used by living organims

Catalysis
A catalyst is a compound that increases the rate of a chemical
reaction
Catalysts lower the activation free energy G‡
Catalysts does not alter G°
Catalysis offers:
-Acceleration under mild conditions
-High specificity Series of Related Reactions Forms a Pathway
-Possibility for regulation

Pathways Are Controlled in Order to Regulate Levels of Metabolites

Reaction coordinate diagram comparing enzyme-catalyzed and uncatalyzed

reactions. In the reaction S → P, the ES and EP intermediates occupy
minima in the energy progress curve of the enzyme-catalyzed reaction. The
terms ΔG‡uncat and ΔG‡cat correspond to the activation energy for the
uncatalyzed reaction and the overall activation energy for the catalyzed
reaction, respectively. The activation energy is lower when the enzyme
catalyzes the reaction.
The Central “Dogma” of Biochemistry
Energy Flows through ATP and redox carriers to couple Catabolic and
Pathway for the flow of genetic information: DNA → RNA → Protein
Anabolic Pathways
 DNA stores information
 RNA transmits information
 Protein function manifests information
Biochemistry CHAPTER 1

Genetic and Evolutionary Foundations

Life on Earth arose 3.5 – 3.8 billion years ago
Formation of self-replicating molecules a key step
 DNA? – Info, Self Template
 Proteins? – Function
 RNA? – Both
Evolutionary Evidence is in DNA sequences TODAY!

RNA World?
RNA can acts both as the information carrier and biocatalyst There is
something fascinating about science. One gets such wholesale returns of
conjecture out of such a trifling investment of fact.

Natural Selection Favors Some Mutations

1. DNA replication is amazingly, but not absolutely, error-free
2. Mutations occur more or less randomly
3. Most mutations are “silent”
4. Many are deleterious
5. Rare mutations that yield an advantage in a given environment are
more likely to be propagated