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Biomolecules
Energetics in biology
Biomolecules inside the cell
Energetics in biology
The production of energy, its storage, and its use are central to the economy
of the cell. Energy may be defined as the ability to do work, a concept
applicable to automobile engines and electric power plants in our physical
world and to cellular engines in the biological world. The energy associated
with chemical bonds can be harnessed to support chemical work and the
physical movements of cells.
Thermal
Several Forms of
Energy Are Important
in Biological Systems
Kinetic energy is the energy of movement,
the motion of molecules, for example.
Radiant
Mechanical
Electric
Potential energy, or stored energy,
is particularly important in the study
of biological or chemical systems.
Chemical potential energy
Concentration gradient
Electric potential
Thermodynamic principles
Open and closed systems
We will review the first and second laws of thermodynamics focusing on
their relationship to energy flow in living organisms.
The first law of thermodynamics states that the total energy of
a system plus its environment remains constant.
Cells Can Transform One Type of Energy into Another:
In photosynthesis, the radiant energy of light is transformed into the chemical potential
energy of the covalent bonds between the atoms in a sucrose or starch molecule.
In muscles and nerves, chemical potential energy stored in covalent bonds is transformed,
respectively, into the kinetic energy of muscle contraction and the electric energy of nerve
transmission.
In all cells, potential energy, released by breaking certain chemical bonds, is used to
generate potential energy in the form of concentration and electric potential gradients.
Similarly, energy stored in chemical concentration gradients or electric potential gradients is
used to synthesize chemical bonds or to transport molecules from one side of a membrane
to another to generate a concentration gradient.
This latter process occurs during the transport of nutrients such as glucose into certain cells
and transport of many waste products out of cells.
The standard unit of energy for biochemists is calorie (1 joule 0.239 calories).
The second law of thermodynamics states that a system and its
surroundings always proceed to a state of maximum disorder or
maximum entropy, a state in which all available energy has been
expended and no work can be performed.
Many biological reactions lead to an increase in order, and thus a decrease
in entropy (S < 0). An obvious example is the reaction that links amino acids
together to form a protein. A solution of protein molecules has a lower
entropy than does a solution of the same amino acids unlinked, because
the free movement of any amino acid in a protein is restricted when it is
bound into a long chain.
reactants
products
All systems change in such a way that free
energy [G] is minimized.
In the conversion of complex foods such as glucose [C6(H2O)6] to simpler
products such as CO2 and H2O, energy conversions, allowed by the first
law of thermodynamics, take place.
The free energy of a chemical system can be defined as G= H -TS,
where H is the bond energy, or enthalpy, of the system; T is its
temperature in degrees Kelvin (K); and S is the entropy, a measure
of its randomness or disorder. If temperature remains constant, a
reaction proceeds spontaneously only if the free-energy change G
in the following equation is negative:
An Unfavorable Chemical Reaction Can Proceed If It Is Coupled with an
Energetically Favorable Reaction
Many processes in cells are energetically unfavorable (G > 0) and will not
proceed spontaneously. Examples include the synthesis of DNA from
nucleotides and transport of a substance across the plasma membrane
from a lower to a higher concentration. Cells can carry out an energyrequiring reaction (G1 > 0) by coupling it to an energy-releasing reaction
(G2 < 0) if the sum of the two reactions has a net negative G.
Energetically unfavorable reactions in cells often are coupled to the
hydrolysis of ATP, as we discuss next.
Hydrolysis of ATP Releases Substantial Free Energy and Drives Many Cellular
Processes
In almost all organisms, adenosine triphosphate, or ATP,
is the most important molecule for capturing,
transiently storing, and subsequently transferring
energy to perform work (e.g., biosynthesis, mechanical
motion). The useful energy in an ATP molecule is
contained in phosphoanhydride bonds, which are
covalent bonds formed from the condensation of two
molecules of phosphate by the loss of water:
An ATP molecule has two key phosphoanhydride
bonds.
Hydrolysis of a phosphoanhydride bond (~) in each
of the following reactions has a highly negative Gº
of about 7.3 kcal/mol:
(ATP Is Generated During Photosynthesis and Respiration)
Biomolecules inside the cell
Cells contain four major families of small organic molecules:
Sugars, Fatty acids, Amino acids, and Nucleotide
Bond type
Sugars:
H
Sugars provide an energy source for cells and are the subunits
of polysaccharides.
The molecules made from sugars , are also called
carbohydrates.
(CH2O)n
I
or H - C - OH
I
O
C
H
C
OH
HO
C
H
H
C
OH
H
C
OH
CH2OH
D-glucose
C6H12O6
w Monosaccharides - simple sugars with multiple OH groups. Based on number of
carbons (3, 4, 5, 6), a monosaccharide is a triose, tetrose, pentose or hexose.
w Disaccharides - 2 monosaccharides covalently linked.
w Oligosaccharides - a few monosaccharides covalently linked.
w Polysaccharides - polymers consisting of chains of monosaccharide or
disaccharide units.
Fatty acids:
Fatty acids, the simplest lipids, consist of a hydrocarbon chain with a
carboxylic acid at one end.
an 16-C fatty acid:
CH3(CH2)14-COONon-polar
polar
Fatty acids are components of cell membranes as well as a source of energy
and are stored in the form of triacylglycerols.
Bipolarity
Cell membrane
Amino acids:
Amino acids are the subunits of proteins
•
•
•
Every amino acid has a similar
basic structure
– NH3CHRCOOH
Except for glycine (R = H), all
amino acids have at least one
asymmetric carbon atom and
exists as two stereoisomers (D
or L)
Only L form exists in proteins
20 common amino acids
Peptide band
Protein structures
•
Organization levels determining protein structure
Level of structure
Basis of Structure
Bonds involved
Primary
Amino acid sequence
Covalent bonds
Secondary
Folding into α helix, β
sheet or random coil
Hydrogen bonds
Tertiary
3D folding of a single
polypeptide
Hydrogen and disulfide
bonds, electrostatic and
hydrophobic
interactions
Quaternary
Association of 2 or more
folded subunits
Same as tertiary
Protein structure
Primary structure
Carbon
Nitrogen
Secondary structure
Tertiary structure
Quaternary structure
Protein function
Functions of membrane proteins:
Outside
Plasma
membrane
Inside
Transporter
Cell surface
identity marker
Enzyme
activity
Cell adhesion
Cell surface
receptor
Attachment to the
cytoskeleton
Nucleotids:
Nucleotids are the subunits of DNA and RNA
A nucleotide is made of 3 components:
A Pentose sugar
A Phosphate group
A Nitogenous base
In DNA the four bases are:
• Thymine (T)
• Adenine (A)
• Cytosine (C)
• Guanine (G)
In RNA the four bases are:
• Uracil (U)
• Adenine (A)
• Cytosine (C)
• Guanine (G)
•
•
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
Chemical structures of the principal bases in nucleic acids:
Five different
nucleotides are used to
build nucleic acids
DNA STRUCTURE
•
hydrogen bonded nucleotides on opposite helices
•
DNA helices are antiparallel
•
carbons on sugar define ends... 5' and 3'
•
pyrimidines bond with purines
• T A
• C G
RNA structure
Ribonucleic acid (RNA). RNA is a single strand of
nucleotides that relays instructions from genes to
ribosomes, guiding the chemical reactions in the
synthesis of amino acids into protein.
mRNA
tRNA
rRNA
Adenosine tri phosphate (ATP)
Energy transfer
Summary
Macromolecules