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BIOCHEMISTRY EXPLAINS
DIVERSE FORMS OF LIFE IN UNIFYING CHEMICAL TERMS
The goal of biochemistry
is to describe how the organized collections of inanimate molecules found in living organisms interact to compose and perpetuate the "living state".
LIVING ORGANISMS
-composed of lifeless inanimate molecules,
-are highly organized structures possessing extraordinary attributes.
Living organisms vs. inanimate matter
1. complicated vs. simple
2. highly organized vs. unorganized
3. PURPOSE: each component has a specific purpose vs. random association
4. ENERGY: capacity to extract energy from environment and transform it to useful energy vs. similar function not exhibited
5. SELF-REPLICATION: precise self-replication vs. no apparent ability to self-replicate
MOLECULAR LOGIC
There can be found a certain "molecular logic" in the living state.
This "logic" can be described by four principle axioms:
Molecular Logic - four principle axioms:
1) There is a basic simplicity in the molecular organization of the cell.

2) The identity of each species of organism is defined and preserved by its possession of characteristic nucleic acids. (DNA, RNA)

3) Living organisms exhibit an underlying principle of "molecular economy".

4) The specificity of molecular interactions within the cells of living organisms results from the structural complementarity of the interacting molecules.
ALL MACROMOLECULES ARE CONSTRUCTED FROM
A FEW SIMPLE COMPOUNDS
Macromolecule simple compounds:
Organic compounds of molecular weight less than about 500, -such as amino acids, nucleotides, and monosaccharides serve as monomeric subunits of the macromolecules known as proteins, nucleic acids, and polysaccharides.
ENERGY PRODUCTION AND CONSUMPTION IN METABOLISM
Organisms are never at equilibrium with their surroundings
THE DYNAMIC STEADY STATE
A dynamic steady state results when the rate of appearance of a cellular component is exactly equal to its rate of disappearance
Energy is defined
as the capacity to do work. -While energy exists in nature in various forms, it can be classified in one of two broad categories ‑ potential energy and kinetic energy.
Potential energy
is the energy possessed by matter because of its composition or condition
Kinetic energy is the energy possessed by matter because of its motion.
is the energy possessed by matter because of its motion.
Thermodynamics is
the study of energy transformations and transfers that accompany physical and chemical changes.
-There are two fundamental laws of nature that are important in thermodynamics and are applicable to living organisms:
two fundamental laws of nature that are important in thermodynamics and are applicable to living organisms:
(1) ENERGY IS CONSERVED, and (2) MATTER TENDS TO ATTAIN A STATE OF MAXIMUM DISORDER. -These laws are defined as the First and Second Laws of Thermodynamics.
The First Law of Thermodynamics states that
the total amount of energy in the universe is constant. That is, energy cannot be created nor destroyed.
The Second Law of Thermodynamics states
that in any spontaneous change, the entropy, or disorder, of the universe increases
During metabolic transductions,
the random-ness of the system plus surroundings (entropy) increases as the potential energy of the complex nutrient molecules decreases.
Living organisms create and maintain their complex, orderly structures using energy extracted from fuels or sunlight.
fuels or sunlight.
-Sunlight is the ultimate source of all biological energy.
-The flow of electrons provides energy for organisms
All of the biochemical reactions involving electron flow are oxidation-reduction reactions; some reactant is oxidized (loses electrons) and another is reduced (gains electrons).
oxidation-reduction reactions; -some reactant is oxidized (loses electrons)
-and another is reduced (gains electrons).
The energy needs of virtually all organisms are provided, directly or indirectly,
by solar energy.

-The flow of electrons in oxidation-reduction reactions underlies energy transductions in living cells.
-Living organisms are interdependent, exchanging energy and matter via the environment.
Thus, living organisms cannot create nor destroy energy, but can
only transform one form of energy into another. In addition, living organisms must expend energy to maintain their high degree of molecular orderliness. In general:
In addition, living organisms must ______ energy to maintain their ________________________.
-expend
-high degree of molecular orderliness
Living organisms create and maintain their essential orderliness at the expense of
their environment (which, in turn, becomes more disordered and random).
Living organisms are _____ systems and thus are ___________ with their environment.
-open systems(they exchange both matter and energy with the environment)
-not in equilibrium
Living organisms exist in a steady state condition
(rate of transfer of matter and energy into the system equals the rate of transfer of matter and energy out of the system).
Living organisms are highly efficient in
handling energy and matter.
Living organisms are essentially isothermal (uniform temperature).
(uniform temperature).
Living organisms utilize _____________ as the major carrier of chemical energy.
adenosine tri-phosphate (ATP)
The amount of energy available to do work is called
the free energy, G.
Energy coupling occurs in both mechanical and chemical processes.
both mechanical and chemical
An activation barrier, representing ____________ must be __________.
-the transition state,
-overcome in converting the reactants into the products.
In biochemical systems, ________ catalyze reactions by _________________.
-enzymes
-lowering the activation barrier.
An enzyme increases the rate of a specific chemical reaction.

Like all catalysts, enzymes are not consumed in the process.
-increases the rate of a specific chemical reaction.
-Like all catalysts, enzymes are not consumed in the process.
ATP IS THE UNIVERSAL CARRIER OF
METABOLIC ENERGY
ATP is the shared chemical intermediate linking
energy-releasing to energy-requiring cell processes.
ATPs role in the cell is
analogous to that of money in the economy;
-it is “earned/produced” in exergonic reactions and
-“spent/consumed” in endergonic ones.
METABOLISM IS REGULATED
Achieves balance and economy.
“Feedback inhibition”
-keeps the production and utilization of each metabolic intermediate in balance.
TYPES OF CELLS
1. Photosynthetic cells ‑ 2.Chemotrophic cells ‑
Photosynthetic cells
‑ utilize sunlight as the main source of energy.
Chemotrophic cells ‑
obtain energy from degradation of high energy organic molecules such as glucose.
All cells contain
-a nucleus or nucleoid region, a
-plasma membrane, and
-cytoplasm
Prokaryotic
("before the nucleus")
Prokaryotic cells
-are relatively simple cells -possessing a single membrane,
(usually surrounded by a rigid cell wall.)
- They possess neither a nucleus nor membranous organelle (such as mitochondria or endoplasmic reticulum).
-They contain only one chromosome consisting of a single molecule of double helical DNA.
prokaryotic cell wall
molecular composition
Composed of a rigid framework of polysaccharide chains cross‑linked with short peptide chains. Lipopolysaccharides coat the outer surface.
prokaryotic cell wall
Properties and Functions
Protects cell against swelling in hypotonic media
prokaryotic cell membrane
molecular composition
Composed of approximately 45% lipid and 55% protein with the lipids forming a continuous non-polar phase. Infoldings of the cell membrane are called mesosomes.
Prokaryotic cell membrane
Properties and functions
A selectively permeable boundary allowing water, nutrients, and metal ions to pass freely. Some enzymes and receptors are located in the membrane.
Prokaryotic Nuclear Zone
molecular composition
The genetic material is a single chromosome of tightly coiled double‑helical DNA.
Prokaryotic Nuclear Zone
Properties and functions
DNA is the carrier of genetic information
Prokaryotic Cytosol
molecular composition
The highly viscous soluble portion of the cytoplasm with a protein concentration exceeding 20%.
Prokaryotic Cytosol
Properties and functions
The cytosol contains enzymes, metabolic intermediates, and inorganic salts.
Prokaryotic cell Ribosome
molecular composition
Composed of two subunits, one large and one small, containing 65% RNA and 35% protein.
Prokaryotic cell Ribosome
Properties and function
Ribosomes are the site of protein synthesis. Messenger RNA binds in the groove between the subunits and specifies the sequence of amino acids in peptide chains.
Prokaryotic cell Storage Granules
Molecular composition
Composed of polymers of sugars or poly‑β‑hydroxybutyric acid.
Prokaryotic cell storage Granules
Properties and function
Used for fuel storage. When needed polymers are enzymatically degraded to yield free glucose or free β‑hydroxybutyric acid.
Eukaryotic
("with a nucleus")
EUKARYOTIC CELLS
-cells are large complex cells possessing several membranes.
-They possess a membrane‑surrounded nucleus and membranous organelle (such as mitochondria or endoplasmic reticulum).
-They contain several chromosomes that undergo mitosis during cell division.
-Many of their metabolic reactions are segregated within structural compartments.
Eukaryotic cell coat
Molecular composition
A flexible and sticky coat found in some cells (such as hepatocytes) composed of acid mucopolysaccharides, glycolipids, and glycoproteins.
Eukaryotic cell coat
Properties and functions
The adhesive properties of cell coats are specific and play a role in cell‑cell recognition and tissue organization.
Eukaryotic cell membrane
Molecular composition
Composed of approximately equal amounts of lipids, and proteins with the lipids forming a continuous non-polar phase.
Eukaryotic cell membrane
properties and functions
A selectively permeable boundary containing active‑transport systems for Na+, K+, glucose, amino acids, other nutrients, and enzymes. Some enzymes and receptors are located in the cell membrane.
Eukaryotic cell Nucleus
Molecular Composition
The nucleus is surrounded by a perinuclear envelope composed of two membranes and a large number of pores. The DNA contained within the nucleus is combined with histones to form chromosomes. The nucleolus, a spherical body located within the nucleus, is rich in RNA.
Eukaryotic cell nucleus
Properties and function
DNA is the carrier of genetic information
Eukaryotic cell Ribosome
molecular composition
Composed of two subunits, one large and one small, containing 65% RNA and 35% protein.
Eukaryotic cell Ribosomes
properties and function
Ribosomes are the site of protein synthesis. Messenger RNA binds in the groove between the subunits and specifies the sequence of amino acids in peptide chains. Associated with the endoplasmic reticulum.
Eukaryotic cells Mitochondrion
molecular composition
Globular structures occupying about 20% of the cytoplasmic volume. Their outer and inner membranes differ in both lipid composition and enzymatic activity. The internal matrix of the mitochondria is rich in enzymes.
Eukaryotic cell Mitochondrion
Properties and function
Carbohydrates, lipids and amino acids are oxidized to CO2and H2O by molecular oxygen to produce energy in the form of ATP.
Eukarytoic cell Golgi Complex
molecular composition
Consists of flattened, single‑membrane vesicles (often stacked). Vacuoles, produced peripherally by a pinching‑off process, contain secretory products.
Eukaryotic cell Golgi complex
properties and function
Functions (1) in the secretion of cell products, and (2) helps to form both the plasma membrane and the membranes of the lysosomes.
Eukaryotic cell microbody (peroxisome)
molecular composition
Single‑membrane vesicles containing catalase, D‑amino acid oxidase, urate oxidase, and other oxidative enzymes.
EUKARYOTIC CELLS
MICROBODY (peroxisome)
PROPERTIES AND FUNCTION:
Microbodies participate in the oxidation of nutrients and the decomposition of hydrogen peroxide into water and oxygen.
EUKARYOTIC CELLS
LYSOSOMES
MOLECULAR COMPOSITION:
Single‑membrane vesicles containing hydrolytic enzymes such as ribonuclease and phosphatase.
EUKARYOTIC CELLS
LYSOSOMES
PROPERTIES AND FUNCTION:
Responsible for the digestion of materials brought into the cell by phagocytosis and/or pinocytosis, and for the digestion of cell components after cell death.
EUKARYOTIC CELLS
ENDOPLASMIC RETICULUM
MOLECULAR COMPOSITION:
The endoplasmic reticulum consists of flattened, single‑membrane vesicles. The inner compartments of the ER, called the cisternea, interconnect and form channels throughout the cytoplasm. Ribosomes are located on the rough surface of the ER.
EUKARYOTIC CELLS
ENDOPLASMIC RETICULUM
PROPERTIES AND FUNCTION:
Provides a highly ramified channel for intracellular transport to the periphery of the cell. As in prokaryotes, protein synthesis occurs in the associated ribosomes.
EUKARYOTIC CELLS
CYTOSOL
MOLECULAR COMPOSITION:
The highly viscous soluble portion of the cytoplasm with a protein concentration exceeding 20%.
EUKARYOTIC CELLS
CYTOSOL
PROPERTIES AND FUNCTION:
The cytosol contains enzymes, metabolic intermediates, and inorganic salts.
prokaryotic Vs Eukaryotic
Size
-generally small (1-10um)
-generally large (5-100um)
prokaryotic Vs Eukaryotic
Genome
-DNA w/ nonhistone protein; genome in nucleoid, not surrounded by membrane.
-DNA complexed with histone and nonhistone proteins in chromosomes; chromosomes in nucleus with membranous envelope.
prokaryotic Vs Eukaryotic
Cell division
-fission or budding; no mitosis
-mitosis, including mitotic spindle; centrioles in many species
prokaryotic Vs Eukaryotic
Membrane-bounded organelles
-absent
-mitochondria, chloroplasts (in plants, some algae), endoplasmic reticulum, golgi complexes, lysosomes (in animals), etc.
prokaryotic Vs Eukaryotic
Nutrition
- absorption; some photosyntheses
-absorption, ingestion; photosyntheses in some species
prokaryotic Vs Eukaryotic
Energy metabolism
-no mitochondria; oxidative enzymes bound to plasma membrane; great variation in metabolic pattern.
-oxidative enzymes packaged in mitochondria; more unified pattern of oxidative metabolism
prokaryotic Vs Eukaryotic
Cytoskeleton
-none
-complex, with microtubules, intermediate filaments, actin filaments
prokaryotic Vs Eukaryotic
intracellular movement
-none
-cytoplasmic streaming, endocytosis, phagocytosis, mitosis, vesicle transport
THE PLASMA MEMBRANE CONTAINS
TRANSPORTERS AND RECEPTORS
Proteins in the plasma membrane serve as
transporters,
signal receptors, and
ion channels.
The size and shape of biomolecules determine
-both the specificity of biological interactions and
-the ultrastructure of living cells.