Transcript Chapter 2 The chemistry of life

Chemistry and Physics of Life
Animal diversity is
shaped (and limited) by
constraints imposed by
a the rules of physics
and chemistry
• Orderliness increases as an organism develops from
a fertilized egg into an adult
• The increase in orderliness requires a constant input
of energy
• When energy intake stops, metabolism stops, and
the order is lost.
Energy
Categories
Figure 2.2
• Animals rely on five forms of energy,
which are interconvertible
Radiant &
Thermal energy
• Radiant energy
travels by waves or
particles
• Chemical reactions
in organisms
produced heat that
must “radiate” out
from animals and
plants
• Thermal regulation
is a big “issue” in
physiology
 Radiant energy
from a cat
Thermal Energy
• An increase in thermal energy results in
movement of molecules, and greatly
affecting the rate of chemical reactions.
• In physiology, rate of chemical reactions is
often synonymous with metabolic rate
• Most chemical reactions involve changes
in thermal energy
• Exothermic reactions – release heat
• Endothermic reactions – absorb heat
Food Webs & energy conversion
1. Radiant energy –
2. Mechanical
energy
3. Electrical energy
4. Thermal energy –
5. Chemical energy
–
Figure 2.3
Electrical energy:
Electrochemical Gradients
Potential and Kinetic energy that results from
the movement of charged particles
1. Organisms invest energy to delay diffusion
2. The unequal distribution of charged particles
is a form of energy storage
3. Gradients can be
chemical, electrical or
both depending on the
nature of the molecule
4. Gradients across a cell
membrane (Membrane
potential) are extremely
important
Electromotive force: emf
• The electrochemical
gradient is maintained
by active transport
across cell
membranes
• The energy of
diffusion is a major
source of potential
physiological
energy & one that is
often overlooked
Temperature Influences Chemical
Reactions
• Increasing
temperature  more
molecules reach
activation energy
• Increases the
likelihood of
endothermic
reactions
Figure 2.5
Chemical Reaction Vocabulary
• Enthalpy – average thermal energy of a
collection of molecules
• Activation energy – energy required for a
molecule to reach a transition state
• Transition state – intermediate structure between
a substrate and a product
• Change in enthalpy (DH) = Hproducts – Hsubstrates
• Exothermic: DH is negative
• Endothermic: DH is positive
Things to keep in mind 
• Chemical reactions
proceed according to the
rules of thermodynamics
• In physiology, as (as in
every science, The law of
conservation of energy
holds firm.
• Entropy – the universe is
becoming more chaotic
DG = DH - TDS
1. If DG is (-); the reaction is exergonic, and the process is
spontaneous
2. If DG is (+), the reaction is Endergonic, and the reaction must be
driven by external energy
Reduction of Free energy drives
chemical and biochemical processes
Free energy is a measure of the ratio
between heat energy, and the change in
entropy
DG = DH - TDS
Consider the breakdown of glucose:
– The large molecule is broken down to carbon
dioxide and water (entropy increases)
– Heat is released to the environment DH is
negative – enthalpy decreases
– Change in free energy will be negative
Exergonic and Enderngonic pairs
Catabolism-degradative, oxidative,
energy yielding
Anabolism-synthetic, reductive,
energy consuming
What is taking place in terms on
enthalpy, entropy and free energy?
DG =?
DG =?
Chemical energy is all about
bonds
• Ionic bonds
• Covalent bonds
• Intermolecular bonds
Covalent Bonds
• Atoms with unpaired electrons can form covalent
bonds with other atoms with unpaired electrons,
i.e., share electrons
• Atoms with more than one unpaired electron can
form multiple covalent bonds
• Geometry of the resultant molecule is influenced
by the bond angle
Figure 2.6
van der Waals Interaction
• Each electron within an atom is constantly
moving
• The nucleus is more negative when the electron
is closer; positive when further away
• Transient dipole – polarity created by asymmetry
in electron distribution
• van der Waals interaction – atom with transient
dipole affects the distribution of electrons in a
second atom
• Effective only over a narrow range of distances
Bond Energy
Chemical bond
energy is the
principle currency
used by organisms
to maintain
homeostasis, to
grow, and to engage
in life activities
Table 2.1
Water
• Most cells are primarily composed of water
• Aquatic organisms live in water
• Cells of terrestrial animals are bathed in
water
• Many physiological processes arose to
meet challenges of the physical and
chemical properties of water
Hydrogen Bonds
• Asymmetric sharing
of electrons between
two atoms
• e.g., Organization of
water molecules
• Hydrogen (+) of
one water molecule
is attracted to
oxygen (-) of another
Figure 2.9
Water: The
Unique Solvent
• The hydrogen bonds
that form between
water molecules
account for some of
the essential — and
unique — properties
of water.
Non-covalent Bonds (Weak Bonds)
• Control macromolecule
structure
• Arise between atoms
with asymmetrical
distributions of
electrons
• Types of intermolecular
bonding
– van der Waals forces
– Hydrogen bonds
– Hydrophobic bonds
Figure 2.8
Functional Groups: order among
chaos
• Combinations of
atoms and bonds
that recur in
biological molecules
Figure 2.7
Binding of ions to Marcromolecules
• A site with a
partial negative
charge attracts
cations
•A site with a
partial positive
charge attracts
cations
Cation binding sites on organic
molecules are generally oxygen atioms
in silicates, carbonyls, carboxylates,
and esthers
The oxygen atom is electron-hungry
and draws electrons from the
surrounding atoms
Hydrophobic Bonds
• Due to mutual aversion to water
• No significant dipoles (polarity)
• Cannot interact with polar
molecules like water
• e.g., oil congealing into droplets
– not attracted to each other,
but repelled by water
Weak Bonds & Temperature
• Weak bonds are sensitive to temperature
because of lower bond energies
• Affects three-dimensional macromolecule
structures
• Denature – macromolecules unfold due to
rising temperature
• e.g., protein, membranes, DNA
Amphipathic compound contain a
polar and nonpolar group.
The hydrophobic, nonpolar “tails”
will “huddle in the center
The polar heads isll face outward
– and interact with the water
The formation of a micelle crucial to the formation of
biological membranes in living cells
Solvents and Solutes
• Solvent – most abundant molecule in a
liquid
• Solute – the other molecules in a liquid
• Solution – solvents and solutes
• In biological systems the solvent is usually
water
Concentration, of solutions, and
colligative properties
Molarity
Moles of solute
1000g solution
Molality
Moles of solute
1000g solvent
1. The amount of solute to solvent is the most
important measure physiologically – so molality
“should be used”
2. Molality is generally inconvenient – most
physiologists use molarity
3. Colligative properties depend on the concentration of solute
particles in a solution.
Water is Affected by
Temperature
• Temperature changes
the organization of
water molecules
• High temperature:
molecules posses
enough thermal energy
to escape the force of
surface tension, i.e., boil
• Low temperature:
stabilize molecules as a
result of additional
hydrogen bonds, i.e., it
solidifies or freezes
Figure 2.11
Density of Water
• Temperature influences the density of
water
• Ice is less dense than liquid water
– Ice has more hydrogen bonds, but molecules
are held further apart
• Water is most dense at 4°C
– Most deep waters are 4°C
– Surface waters can be colder or warmer
Water is a Very Stable Liquid
• High melting point
• High boiling point
• High heat of vaporization – amount of
energy to cause liquid water to boil
Table 2.2
Solutes can Dissolve in Water
• Solutes form
hydrogen bonds
with water
molecules
• Hydration shell –
solute surrounded
by water molecules
Figure 2.12
Water dissolves polar molecules
What's in your water?
• A compound added to gasoline to help it
burn more cleanly
• Methyl Tertiary Butyl Ether (MTBE).
Solutes Affect Properties of
Water
• Colligative properties
• Decrease freezing point
• Increase
– Boiling point
– Vapor pressure
– Osmotic pressure
• Depend on the number of solutes,
not their size or charge
Solutes Impose Osmotic Pressure
• Semipermeable membrane – allow some
molecules to cross while restricting others
• Osmotic pressure – force associated with the
movement of water
• Osmolarity – ability of solution to induce water to
cross a membrane
Figure 2.13
Relative Osmolarity and Tonicity
Figure 2.14
pH and the Ionization of Water
• Dissociation of a water
molecule into ions
– H:O:H  H:O:- + H+
• pH = -log10 [H+]
– Brackets denote
concentration
• Pure water is pH 7
(-log 10-7)
Figure 2.5
Neutrality
• Neutrality - [H+] = [OH-] or pH = pOH
• Affected by temperature
– pH at neutrality (pN) varies inversely with
temperature
• 5°C: pN = 7.28
• 25°C: pN = 7.00
• 45°C: pN = 6.72
Acids and Bases Alter the pH of
Water
• Acids – release protons   pH
– HA  H+ + A-
• Bases – accept protons  pH
• Mass action ratio = ([H+] X [A-]) / [HA]
• Equilibrium constant (Keq) - [HA] reaches a
minimum and [H+] and [A-] reach a maximum
– pK = -log10 Keq
– pK = pH –log [A-] / [HA]
• pK reflects the strength of acids or bases
Strength
of Acids
and
Bases
Table 2.3
pH Affects Ionization State
Figure 2.16
Temperature Affects Ionization
State
• pK increases as temperature
decreases
• Each ionizable groups has a
characteristic sensitivity to
temperature
 DpK/°C
Buffers Limit Changes in pH
• Buffer – chemical
found in solution that
dampens the effect of
added acid or base
• Mixture of protonated
and deprotonated
molecules
• Most buffers rely on
weak acids
• Buffers work only over
a particular range of
pH values
Figure 2.17
Biomolecules
•
•
•
•
•
Four main types
Carbohydrates
Lipids
Proteins
Nucleic acids
• Metabolism – Sum of metabolic
pathways for the interconversion of
these macromolecules and their
breakdown for energy
Carbohydrates
• Lots of hydroxyl (-OH) groups
• No other general structural
features
• Glucose is the most common
carbohydrate in animal diets
• Energy metabolism
• Biosynthesis: precursor to
most other carbohydrates
Monosaccharides
• Used for energy
and biosynthesis
• Small
carbohydrates with
three to seven
carbons – six is
most common
Figure 2.18
Disaccharides
• Two monosaccharides connected by a covalent bond
• Broken down when used
Figure 2.19
Carbohydrates + other
Macromolecules
• Glycosylation – addition of carbohydrates
to other macromolecules
• Alters molecular profile of the
macromolecule
• e.g., glycolipids, glycoproteins
– Both are typically found in plasma
membranes and the extracellular fluid
Complex Carbohydrates
•
•
•
•
Polysaccharides
Long chain of monosaccharides
Energy storage or structural molecules
e.g., glycogen, starch, cellulose
Complex Carbohydrates , Cont.
Figure 2.20
Complex Carbohydrates, Cont.
• Structural
carbohydrates
– Chitin –
exoskeleton of
arthropods
– Hyaluronate –
gel-like spacer
between cells in
vertebrates
Figure 2.21
Lipids
• All are hydrophobic
• Composed of a carbon
backbone
– Linear – aliphatic
– Ring – aromatic
• e.g., fatty acids, triglycerides,
phospholipids, steroids
Fatty Acids
• Long chains of
carbon ending with a
carboxyl group
• Saturated –
no double bonds
• Unsaturated –
one or more double
bonds
Figure 2.22
Triglycerides
• Fatty acids are stored as
triglycerides
• Fatty acids are esterified to a
glycerol backbone
– e.g., Mono-,di-, tri-acylglycerol
• High concentration in lipids
Figure 2.23
Phospholipids
• Dominate biological
membranes
• Constructed from
diacylglycerol
• Two classes
– Phosphoglycerides
– Sphingolipids
Phospholipids, Cont.
Figure 2.24a
Phospholipids, Cont.
Figure 2.24b
Steroids
• Four hydrocarbon
rings
• Synthesis involves
many intermediates
Figure 2.25
Proteins
• Make up almost half of cell volume
(excluding water)
• Mediate all cellular processes
• Contribute to cell structure
• Have complex structure
Amino Acids
• Proteins are polymers of amino acids
• Amino acids: amino group (-NH2) and a
carboxylic acid group (-COOH)
• Termed a-amino acids because -NH2 and
-COOH are located on the 1st carbon
• Distinguished by side groups (R)
• Can be nonpolar (hydrophobic), polaruncharged (hydrophilic) and polarcharged (hydrophilic)
Amino Acids, Cont.
Figure 2.26 (1 of 2)
Amino Acids, Cont.
Figure 2.26 (2 of 2)
Protein Structure
Figure 2.28
Primary Structure
Figure 2.27
• Linear sequence of amino acids joined by covalent
peptide bonds between the carboxyl and amino
group
Secondary Structure:
a-helix & b-sheet
Results from hydrogen bonding
between the carboxyl oxygen
and the hydrogen of the amine
group. It is the most stable
configuration
hair, fingernails, claws, horns
Tertiary Structure
• Covalent bonds
(disulfide bonds) and
weak bonds (van der
Waals forces, ionic
bonds, and hydrogen
bonds)
Figure 2.30
Quaternary Structure
• Multiple polypeptide chains
• Dimer – 2 subunits
– Homodimer – identical proteins
– Heterodimer – different proteins
• Trimer – 3 subunits
• Tetramer – 4 subunits
Molecular chaperones and Stress
proteins
• A family of proteins
that helps the
formation of the
folded structure,
and for the
preservation of the
complex structure
• Commonly called
heat-shock proteins
Nucleic Acids
• Two types
• DNA – deoxyribonucleic acid
– Genetic blueprint
• RNA – ribonucleic acid
– Read and interpret DNA to make protein
– Three main forms
• Transfer RNA (tRNA)
• Ribosomal RNA (rRNA)
• Messenger RNA (mRNA)
Nucleic Acids, Cont.
• Polymers of nucleotides linked by
phosphodiester bonds
• Nitrogenous base (4 types) attached to
sugar linked to a phosphate
– Cytosine
– Adenine
– Guanine
– Thymine (DNA only)
– Uracil (RNA only)
Nucleic Acids, Cont.
Figure 2.32 (1 of 2)
Nucleic Acids, Cont.
Figure 2.32 (2 of 2)
DNA
• Nucleotides can form bonds
with only one other nucleotide
– A + T: two hydrogen bonds
– G + C: three hydrogen bonds
1. Doublestranded a-helix
2. Two strands are
linked by
hydrogen bonds
DNA Structure
Figure 2.33
Histones
• Strand of mammalian DNA is several meters long
• DNA is compressed by DNA-binding proteins
(histones)
• Advantages of compression by histones
– Large amounts of DNA fit into small volumes
– Reduces damage caused by radiation and chemicals
• Must be uncompressed for DNA and RNA synthesis
Figure 2.34
DNA Organization
• Genome - entire
collection of DNA within a
cell
• Chromosome – separate
segments of DNA
• Genes – DNA sequence
within a chromosome
• Exons – genes that
encode RNA
• Introns – interspersed
DNA sections
Figure 2.35
Genome Size
• Highly variable
• Little relationship
between genome
size and animal
complexity
Figure 2.36
Enzymes
•
•
Catalysts that accelerate chemical
reactions
Enzymes have three properties
1. Active at low concentrations
2. Increase the rate of reactions but are not
altered
3. Do not change the products
•
•
Most are made of proteins
Some are made of RNA (ribozymes)
Cofactors
• Nonprotein components of enzymes
• Many are loosely associated with enzymes
• Prosthetic group – cofactor covalently bonded
into the enzyme
• Coenzymes – organic cofactors usually
derived from vitamins
• Inorganic ion cofactors – copper, iron,
magnesium, zinc
Reaction Acceleration
• Enzymes accelerate reactions by reducing
reaction activation energy (EA)
• Uses the same substrate and yields the
same product
• Reaction follows a different path with a
different intermediate at the transition state
• S + E  ES  ES*  EP*  EP  E + P
• Active site – location in enzyme where
substrate binds
Reaction Acceleration, Cont.
Figure 2.37
Enzyme Kinetics
• Conditions that influence the rate of enzymatic reactions
• Not the fastest rate, but the appropriate rate
• Changing the concentration of substrate and product will
affect reaction rates
Figure 2.38
Michaelis-Menton Rectangular Hyperbola
•
•
•
•
V = Vmax X [S] / ([S] + Km)
V = initial velocity
Vmax = maximum velocity
Km = indicator of affinity of enzyme for the substrate
Figure 2.39
Sigmoidal Relationships
• Homotropic enzymes – show a sigmoidal relationship
between V and [S]
• Cooperativity – enzymes show increased affinity for S with
increasing [S]
• Hill coefficient – degree of cooperativity (slope at inflection)
Figure 2.41
Environmental Effects
• Enzyme activity is
affected by
temperature, pH,
salinity, and hydrostatic
pressure
Figure 2.42
Environmental Effects, Cont.
• Enzymes are affected in different ways
• Changes in weak bonds alter three-dimensional
structure
• Changes in ionization state of amino acids within
the active site
• Changes in the ability of the enzyme to undergo
structural changes necessary for catalysis
Non-catalytic Molecules
• Do not participate directly in catalysis, but
can alter enzyme kinetics
Figure 2.44a, b
Non-catalytic Molecules, Cont.
Figure 2.44c
Energy Storage &Reducing Energy
• Two main forms of storage:
– Reducing energy
– High energy bonds
• The Reducing equivalents are a
vitamin + nucleotide
– e.g., NAD, NADP, FAD, FMN
• Oxidoreductases are enzymes
that store energy in reducing
equivalents by converting them
from an oxidized (energy-poor)
form to a reduced (energy-rich)
form
– e.g., NAD+  NADH
• Redux status – reducing energy
within a cell = reduced
form/oxidized form
– e.g., [NADH/NAD+]