Transcript Chemistry Comes Alive

Chemistry Comes
Alive
The Chemistry of Life
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Atoms, Ions and Molecules
Water and Mixtures
Energy and Chemical Reactions
Organic compounds
Matter
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The “stuff” of the universe
Anything that has mass and takes up
space
States of matter
Solid – has definite shape and volume
 Liquid – has definite volume, changeable
shape
 Gas – has changeable shape and volume
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The Chemical Elements
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Element
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simplest form of matter with unique chemical
properties
Each element has unique physical and
chemical properties
Physical properties – those detected with our
senses
 Chemical properties – pertain to the way
atoms interact with one another
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Major Elements of the
Human Body
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98.5% of body weight consists of
Oxygen (O)
 Carbon (C)
 Hydrogen (H)
 Nitrogen (N)
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Lesser and Trace Elements
of the Human Body
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Lesser elements make up 3.9% of the
body and include:
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Calcium (Ca), phosphorus (P), potassium (K),
sulfur (S), sodium (Na), chlorine (Cl),
magnesium (Mg), iodine (I), and iron (Fe)
Trace elements make up less than 0.01%
of the body
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They are required in minute amounts, and
are found as part of enzymes
Periodic Table of the Elements
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Atomic number of each element
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number of protons in its nucleus
Periodic table
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letter symbols of elements arranged by
atomic number
http://pearl1.lanl.gov/periodic/default.htm
Atomic Structure
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Nucleus - center of atom contains
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protons: positive charge, mass of 1 amu
neutrons: neutral charge, mass of 1 amu
atomic mass = total # of protons + neutrons
Electron shells
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electrons: negative charge
# of electrons = # of protons, atoms have neutral
charge
electrons further from nucleus have higher energy
valence electrons are in the outermost shell
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interact with other atoms
determine chemical behavior
octet rule - atoms react to obtain a stable number of 8 valence
electrons
Bohr Planetary Model of an
Atom
Models of Some Elements
p+ represents protons, no represents neutrons
Isotopes and Radioactivity
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Isotopes
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elements that differ in the number of neutrons
 1H, 2H, 3H
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extra neutrons result in increased atomic weight
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have no change in chemical behavior
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“heavy water”
same valence electrons
Atomic weight
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Average atomic mass of the mixture of isotopes of
an element found in a sample
Isotopes of Hydrogen
–radioisotopes decay to stable isotopes releasing radiation
Figure 2.3
Radioisotopes and
Radioactivity
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Isotopes
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Radioisotopes
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same chemical
behavior, differ in
physical behavior
unstable isotopes
Radioactivity
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radioisotopes decay
to stable isotopes
releasing radiation
Marie Curie
Ionizing Radiation
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High energy
Ejects electrons from atoms
Destroys molecules and produces free radicals
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sources include:
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 particle 
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2 protons + 2 neutrons can’t penetrate skin
 particle 
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UV light, X rays, nuclear decay (, , )
free electron - penetrates skin a few millimeters
 particle 
high energy, penetrating; very dangerous
Ionizing Radiation 2
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Physical half-life
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time for 50% of atoms to decay
90Sr - 28 yr.
40K - 1.3 billion years
Biological half-life
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time for 50% of atoms to disappear from the body
function of decay and physiological clearance
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Cesium 137 - physical half-life -- 30 years
- biological half-life -- 17 days
Radiation exposure
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background radiation
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radon gas from decay of uranium in granite
cosmic rays
Molecules and Chemical Bonds
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Molecules
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Compounds
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two or more atoms of different elements
covalently bonded
Molecular formula
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two or more atoms of same element covalently
bonded
itemizes each element present and its quantity
Structural formula
shows arrangement of atoms
 needed to show structural isomers
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Concentration of Solutions
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Percent, or parts per 100 parts
Molarity, or moles per liter (M)
Mole – Avagadro’s number of molecules
 6.02 X 1023
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A mole of an element or compound is
equal to its atomic or molecular weight
(sum of atomic weights) in grams
Types of Chemical Bonds
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Ionic
Covalent
Hydrogen
Chemical Bonds
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Electron shells, or energy levels, surround the
nucleus of an atom
Bonds are formed using the electrons in the
outermost energy level
Valence shell – outermost energy level
containing chemically active electrons
Octet rule – except for the first shell which
is full with two electrons, atoms interact in a
manner to have eight electrons in their
valence shell
Chemically Inert Elements
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Inert elements have their outermost energy level
fully occupied by electrons
Figure 2.4a
Chemically Reactive Elements
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Reactive
elements do
not have their
outermost
energy level
fully occupied
by electrons
Figure 2.4b
Ions
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Ions - carry a charge, unequal
numbers of protons and electrons
Ionization transfer of
electrons from
one atom to
another (
stability of
valence shell)
Anions and Cations
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Anion - atom gained electron, net negative
charge
Cation - atom lost an electron, net positive
charge
Ionic Bonds
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Attraction of oppositely charged ions to each
other forms an ionic bond - no sharing of electrons
Ionic bonds are weak and dissociate in water
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These compounds tend to form crystals...
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Formation of an Ionic Bond
Figure 2.5a
Covalent Bonds
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Formed by sharing
valence electrons
Types of covalent
bonds
 single covalent
bond
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double covalent
bond
Triple covalent
bond
Polar and Nonpolar Molecules
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Electrons shared equally between atoms
produce nonpolar molecules
Unequal sharing of electrons produces
polar molecules
Atoms with six or seven valence shell
electrons are electronegative
Atoms with one or two valence shell
electrons are electropositive
Comparison of Ionic, Polar
Covalent, and Nonpolar Covalent
Bonds
Figure 2.8
Hydrogen Bonds
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Weakest of the bonds
Attraction between polar molecules – no
sharing of electrons
Greatest physiological importance
properties of water
 shapes of complex molecules
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proteins, DNA
Hydrogen Bonding in Water
The Chemistry of Life
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Atoms, Ions and Molecules
Water and Mixtures
Energy and Chemical Reactions
Organic compounds
Adhesion and Cohesion
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Adhesion - attraction between one
substance and another substance
Cohesion - attraction between one
substance and itself
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water is very cohesive due to hydrogen bonds
Surface tension
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elastic surface film caused by the attraction of
molecules at the surface from those below
Thermal Stability of Water
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Heat capacity: amount of heat required to raise
the temperature of 1g of a substance by 1°C
Calorie: amount of heat required to raise the
temperature of 1g of water by 1°C
Water stabilizes internal temperature of the
body
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high heat capacity
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its hydrogen bonds inhibit increased temperature (molecular
motion) caused by increased heat
effective coolant
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1 ml of perspiration removes 500 calories from the body
Properties of Water
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Reactivity – is an important part of
hydrolysis and dehydration synthesis
reactions
Cushioning – resilient cushion around
certain body organs
PLAY
InterActive Physiology®:
Fluid, Electrolyte, and Acid/Base Balance: Introduction to Body Fluids
Mixtures and Solutions
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Mixtures – two or more components
physically intermixed (not chemically
bonded)
Solutions – homogeneous mixtures of
components
Solvent – substance present in greatest
amount
 Solute – substance(s) present in smaller
amounts
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Solvency
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Solvency - ability to dissolve matter
Hydrophilic - charged substances that
dissolve easily in water
Hydrophobic - neutral substances that do
not easily dissolve in water
Water is the universal solvent, important
for metabolic reactions and transport of
substances
Water as a Solvent
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Water molecules overpower the ionic bond above
between Na+Cl- by forming hydration spheres.
Note orientation of water molecules: negative pole
faces Na+, positive pole faces Cl-
Mixtures
Substances that
are physically
blended but not
chemically
combined
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Solutions
Colloids
Suspensions
Solutions
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Solute < 1nm
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pass through
membranes
Transparent
e.g. copper sulfate
solution
Colloids
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Particles 1 to
100nm
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to large to pass
through membranes
Cloudy
e.g. milk protein
Suspensions
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Particles >100nm
Cloudy or opaque
Separate on
standing
e.g. blood cells
Measures of Concentration
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Weight per Volume
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weight of solute in a given volume of solution
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e.g. IV saline contains 8.5 g/L NaCl
Percentages
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weight or volume of solute in solution
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e.g. IV D5W (5% w/v dextrose in distilled water)
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5 grams of dextrose in add 100ml water
Molarity
number of moles of solute/liter in solution
 physiologic effects of a chemical based on
the number of molecules in solution
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Salts
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Inorganic compounds
Contain cations other than H+ and anions
other than OH–
Are electrolytes; they conduct
electrical currents
Acids and Bases
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Acids release H+ and are therefore
proton donors
HCl  H+ + Cl –
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Bases release OH– and are proton
acceptors
NaOH  Na+ + OH–
Acid-Base Concentration
(pH)
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Acidic solutions have higher H+
concentration and therefore a lower pH
Alkaline solutions have lower H+
concentration and therefore a higher
pH
Neutral solutions have equal H+ and OH–
concentrations
pH
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pH - based on the molarity of H+ on a
logarithmic scale
pH = -log [H+]
 for molarity of H+ = 100,10-1,10-2,etc.
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pH = - log [100] = 0, - log [10-1] = 1, etc.
a change of one number on the pH scale
therefore represents a 10 fold change in H+
concentration
Our body uses buffers to resist any
change in pH
pH Scale
Buffers
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Systems that resist abrupt and large
swings in the pH of body fluids
Carbonic acid-bicarbonate system
Carbonic acid dissociates, reversibly
releasing bicarbonate ions and protons
 The chemical equilibrium between carbonic
acid and bicarbonate resists pH changes in
the blood
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PLAY
InterActive Physiology®:
Fluid, Electrolyte, and Acid/Base Balance: Acid/Base Homeostasis
The Chemistry of Life
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Atoms, Ions and Molecules
Water and Mixtures
Energy and Chemical Reactions
Organic compounds
Work and Energy
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Energy - the capacity to do work
Kinetic energy - energy of motion
Potential energy- inherent energy due
to an objects position or internal
state
Chemical energy - potential energy
stored in the molecular bonds
Electromagnetic energy - kinetic
energy of photons:
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light, infrared, UV, X rays +  rays
Chemical Reactions
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Occur when chemical bonds are formed,
rearranged, or broken
Are written in symbolic form using
chemical equations
Chemical equations contain:
Number and type of reacting substances,
and products produced
 Relative amounts of reactants and products
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Examples of Chemical
Reactions
Patterns of Chemical
Reactions
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Combination reactions: Synthesis reactions
which always involve bond formation
A + B  AB
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Decomposition reactions: Molecules are
broken down into smaller molecules
AB  A + B
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Exchange reactions: Bonds are both made
and broken
AB + C  AC + B
Energy Flow in Chemical
Reactions
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Exergonic reactions – reactions that
release energy
Endergonic reactions – reactions whose
products contain more potential energy
than did its reactants
Metabolism
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All the chemical reactions of the body
Catabolism
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energy releasing (exergonic) decomposition
reactions
Anabolism
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energy releasing (endergonic) synthesis
reactions
Reaction Rates
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Basis for chemical reactions is molecular
motion and collisions
Reaction Rates affected by:
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concentration
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temperature
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more concentrated, more collisions, faster rx
higher temperature, greater collision force, faster rx
catalysts
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speed up reactions without permanent change to itself
biological catalysts are enzymes
Oxidation-Reduction (Redox)
Reactions
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Reactants losing electrons are electron
donors and are oxidized
Reactants taking up electrons are
electron acceptors and become reduced
Energy Flow in Chemical
Reactions
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Exergonic reactions – reactions that
release energy
Endergonic reactions – reactions whose
products contain more potential energy
than did its reactants
The Chemistry of Life
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Atoms, Ions and Molecules
Water and Mixtures
Energy and Chemical Reactions
Organic compounds
Organic Compounds
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Molecules unique to living systems
contain carbon and hence are organic
compounds
They include:
Carbohydrates
 Lipids
 Proteins
 Nucleic Acids
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Organic Molecules: Carbon
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Bonds readily with other carbon atoms,
hydrogen, oxygen, nitrogen, sulfur
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needs 4 more valence electrons
Can form rings or long carbon chains that
serve as the backbone for organic
molecules
Functional Groups
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Groups of atoms attach
to carbon backbone
Determine the
properties of organic
molecules
Monomers and Polymers
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Monomers
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subunits of macromolecules
DNA has 4 different monomers (nucleotides)
 proteins have 20 different monomers (amino acids)
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Polymers
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series of monomers bonded together
Polymerization
the bonding of monomers together to form a
polymer
 caused by a reaction called dehydration
synthesis
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Monomers and Polymers
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Monomers
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subunits of macromolecules
DNA has 4 different monomers (nucleotides)
 proteins have 20 different monomers (amino acids)
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Polymers
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series of monomers bonded together
Polymerization
the bonding of monomers together to form a
polymer
 caused by a reaction called dehydration
synthesis
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Hydrolysis
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Splitting a polymer (lysis) by the addition
of a water molecule (hydro)
Digestion consists of hydrolysis reactions
Carbohydrates
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Contain carbon, hydrogen, and oxygen
Their major function is to supply a
source of cellular food
Examples:
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Monosaccharides or simple sugars
Figure 2.13a
Organic Molecules:
Carbohydrates
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Hydrophilic organic molecule
General formula
(CH2O)n , n = number of carbon atoms
 for glucose, n = 6, so formula is C6H12O6
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Names of carbohydrates
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word root sacchar- or the suffix -ose often
used
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monosaccharide or glucose
Monosaccharides
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Simplest carbohydrates
General formula is C6H12O6
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structural isomers
Three major
monosaccharides
glucose, galactose and
fructose
 mainly produced by
digestion of complex
carbohydrates
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Disaccharides
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Pairs of
monosaccharides
Three major
disaccharides
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sucrose
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lactose
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glucose + fructose
glucose + galactose
maltose
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glucose + glucose
Polysaccharides
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Starch, cellulose and glycogen
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long chains of glucose form these polysaccharides
Starch produced by plants is digested by amylase
Cellulose gives structure to plants, fiber to our
diet
Polysaccharides
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Glycogen is an energy storage polysaccharide
produced by animals
Liver cells synthesize glycogen after a meal to
maintain blood glucose levels
Carbohydrate
Functions
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Source of energy
Conjugated carbohydrates
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glycolipids
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external surface of cell membrane
glycoproteins
external surface of cell membrane
 mucus of respiratory and digestive tracts
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proteoglycans
carbohydrate component dominant
 cell adhesion, gelatinous filler of tissues (eye) and
lubricates joints
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Lipids
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Contain C, H, and O, but the proportion
of oxygen in lipids is less than in
carbohydrates
Examples:
Neutral fats or triglycerides
 Phospholipids
 Steroids
 Eicosanoids
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Fatty Acids
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Chain of usually 4 to 24 carbon atoms
Carboxyl (acid) group on one end and a
methyl group on the other
Polymers of two-carbon acetyl groups
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Fatty Acids
Saturated fatty acid - carbon atoms
saturated with hydrogen
Unsaturated fatty acid - contains C=C
bonds that could bond more hydrogen
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Fatty Acids
Saturated fatty acid - carbon atoms
saturated with hydrogen
Unsaturated fatty acid - contains C=C
bonds that could bond more hydrogen
Triglyceride Synthesis (2)
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Triglycerides called neutral fats
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fatty acids bond with their carboxyl ends, therefore no
longer acidic
Triglycerides
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Hydrolysis of fats occurs by lipase enzyme
Triglycerides at room temperature
liquid called oils, often polyunsaturated fats
from plants
 solid called fat, saturated fats from animals
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Function - energy storage
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also insulation and shock absorption for organs
Phospholipids
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Amphiphilic character
Hydrophobic “tails” similar to neutral fats
with two fatty acids attached to glycerol
Hydrophilic “head” differs from neutral fat
with the third fatty acid replaced with a
phosphate group attached to other
functional groups
A Phospholipid - Lecithin
Steroids
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Cholesterol
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other steroids derive from cholesterol

cortisol, progesterone, estrogens, testosterone
and bile acids
required for proper nervous system
function and is an important component of
cell membranes
 produced only by animals
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85% naturally produced by our body
 only 15% derived from our diet
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Eicosanoids
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Derived from arachidonic acid (a fatty acid)
Function as chemical signals between cells
Includes prostaglandins

role in inflammation, blood clotting, hormone action,
labor contractions, control of blood vessel diameter
Cholesterol
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All steroids have this 4 ringed structure
with variations in the functional groups and
location of double bonds
Representative Lipids Found
in the Body
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Neutral fats – found in subcutaneous tissue and
around organs
Phospholipids – chief component of cell
membranes
Steroids – cholesterol, bile salts, vitamin D, sex
hormones, and adrenal cortical hormones
Fat-soluble vitamins – vitamins A, E, and K
Eicosanoids – prostaglandins, leukotriens, and
thromboxanes
Lipoproteins – transport fatty acids and
cholesterol in the bloodstream
Organic Molecules: Proteins
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Polymer of amino acids
20 amino acids
identical except for -R
group attached to central
carbon
 amino acid properties
determined by -R group
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The amino acids in a
protein determine its
structure and function
Amino Acids
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Building blocks of protein, containing an
amino group and a carboxyl group
Amino acid structure
PLAY
InterActive Physiology®:
Fluid, Electrolyte, and Acid/Base Balance: Introduction to Body Fluids
Amino Acids
Figure 2.15a-c
Amino Acids
Figure 2.15d, e
Peptides
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A polymer of 2 or more amino acids
Named for the number of amino acids
they contain
dipeptides have 2, tripeptides have 3
 oligopeptides have fewer than 10 to 15
 polypeptides have more than 15
 proteins have more than 100
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Dehydration synthesis creates a peptide
bond that joins amino acids
Dipeptide Synthesis
Protein

Macromolecules composed of
combinations of 20 types of amino acids
bound together with peptide bonds
Figure 2.16
Structural Levels of Proteins
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Primary – amino acid sequence
Secondary – alpha helices or beta
pleated sheets
PLAY
Chemistry of Life:
Proteins: Secondary Structure
Structural Levels of Proteins
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Tertiary – superimposed folding of
secondary structures
Quaternary – polypeptide chains linked
together in a specific manner
PLAY
Chemistry of Life:
Proteins: Tertiary Structure
PLAY
Chemistry of Life:
Proteins: Quaternary Structure
Fibrous and Globular Proteins

Fibrous proteins
Extended and strandlike proteins
 Examples: keratin, elastin, collagen, and
certain contractile fibers

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Globular proteins
Compact, spherical proteins with tertiary
and quaternary structures
 Examples: antibodies, hormones, and
enzymes
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Protein Denuaturation

Reversible
unfolding of
proteins due
to drops in
pH and/or
increased
temperature
Figure 2.18a
Protein Denuaturation

Irreversibly denatured proteins cannot
refold and are formed by extreme pH
or temperature changes
Figure 2.18b
Characteristics of Enzymes
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Most are globular proteins that act as
biological catalysts
Holoenzymes consist of an apoenzyme
(protein) and a cofactor (usually an ion)
Enzymes are chemically specific
Frequently named for the type of
reaction they catalyze
Enzyme names usually end in -ase
Lower activation energy
Characteristics of Enzymes
Figure 2.19
Mechanism of Enzyme Action
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Enzyme binds with substrate
Product is formed at a lower activation
energy
Product is released
PLAY
How Enzymes Work
Nucleic Acids

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(C), thymine (T), and uracil (U) Composed of
carbon, oxygen, hydrogen, nitrogen, and
phosphorus
Their structural unit, the nucleotide, is
composed of N-containing base, a pentose
sugar, and a phosphate group
Five nitrogen bases contribute to nucleotide
structure – adenine (A), guanine (G), cytosine
Two major classes – DNA and RNA
Deoxyribonucleic Acid (DNA)

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Double-stranded helical molecule found
in the nucleus of the cell
Replicates itself before the cell divides,
ensuring genetic continuity
Provides instructions for protein
synthesis
Structure of DNA
Figure 2.21a
Structure of DNA
Figure 2.21b
Ribonucleic Acid (RNA)
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Single-stranded molecule found in both
the nucleus and the cytoplasm of a cell
Uses the nitrogenous base uracil instead
of thymine
Three varieties of RNA: messenger
RNA, transfer RNA, and ribosomal RNA
Adenosine Triphosphate
(ATP)


Source of immediately usable energy
for the cell
Adenine-containing RNA nucleotide with
three phosphate groups
Adenosine Triphosphate
(ATP)
Figure 2.22
How ATP Drives Cellular
Work
Figure 2.23