Download Atomic Structure (Bohr or Planetary Model)

Chemical Bonds
• The interaction between 2 atoms may result in the
formation of a chemical bond whereby 2 atoms are
chemically linked to one another
– 2 major types
• Ionic
• Covalent
• Atoms bond with one another to become stable
– an atom is stable when the valence shell is
completely full (satisfying the “octet rule”)
• Groups of atoms that are associated with each other
through bonds are called molecules
– chemicals that are LARGER and structurally more
CoMpLe
X
than individual atoms
Molecules
• Molecules
– two or more atoms bonded together
• carbon dioxide (CO2), Glucose (C6H12O6), water
(H2O), sodium chloride (NaCl)…
Nonpolar and Polar Molecules
• Nonpolar molecules include those containing a
high number of nonpolar covalent bonds and few
polar covalent bonds (very little or no O and/or N)
– lipids (fats)
• uncharged (neutral) molecules
• Polar molecules include those containing a
moderate number of polar covalent bonds
(moderate amounts of O and/or N)
• include every other substance:
– carbohydrates, proteins, nucleic acids, water…
– ions (cations and anions)
• charged molecules
Hydrogen Bonds
• Electrical attraction between a polar covalently bound
H (has a partial positive charge) and a covalently
bound electronegative atom (O/N) (has a partial
negative charge)
• Too weak to bind atoms together
– serve as intramolecular (within molecule) bonds
• aids in the stabilization of very large molecules
• observed in proteins and nucleic acids
– serve as intermolecular (between molecules) bonds
• holds 2 or more molecules in close proximity to
one another
• observed in between water molecules
Hydrogen Bonds in Water (intermolecular)
Water
• The most abundant molecule of the human body
– 70% of body mass (weight) is attributed to water
• Polar substances mix easily with other polar
substances, but do not mix with nonpolar substances
(REMEMBER THIS)
• Nonpolar substances mix easily with other nonpolar
substances, but do not mix with polar substances
(REMEMBER THIS)
– like dissolves like
• The majority of the chemicals found in the body are
polar, however lipids are molecules essential for
proper functioning of the body
Polarity (Water vs Lipids)
• All polar chemicals mix with water and are considered
to be hydrophilic (water loving)
– polar chemicals that mix with water will not mix with
lipids and are considered to be lipophobic (lipid
fearing)
• All nonpolar chemicals mix with lipids and are
considered to be lipophilic (lipid loving)
– Nonpolar chemicals that associate with lipids will
not mix with water and are considered to be
hydrophobic (water fearing)
• Polar = hydrophilic = lipophobic
• Non-polar = hydrophobic = lipophilic
Properties of Water
• Solvency
– ability to dissolve matter
• because water is the most abundant compound
in the body it is the universal solvent
• environment for all metabolic reactions
• provides a means for the transport of substances
from one location in the body to another
• Adhesion and Cohesion
– molecules of water “stick” to themselves and other
types of molecules
• due to hydrogen bonds
• High heat capacity
• prevents rapid increases or decreases in
temperature
Biochemical Reactions
• The functioning of the body (physiology) occurs as the
organic molecules of the body react with one another
• Written symbolically with chemical equations
– relative amounts of reactants (starting chemicals)
and products (finishing chemicals)
– number and type of reacting substances, and
products produced
• C6H12O6 + 6O2  6H2O + 6CO2
• Chemical reactions occur when covalent bonds in a
molecule are formed or broken
– the formation of a covalent bond uses energy
– the breaking of a covalent bond releases energy
• All chemical reactions are theoretically reversible
A + B ↔ AB CO2 + H2O ↔ H2CO3 ↔ HCO3- + H+
Work and Energy
• Energy
– capacity to do work
• Kinetic energy
– energy of motion
• Potential energy
– energy due to object’s position
Energy Sources
• Energy sources that the body uses includes:
– Chemical
• stored in the covalent bonds of energy-rich
molecules (potential)
– Electrical
• the movement of ions (potential and kinetic)
– Heat
• causes molecules to move (kinetic)
– Mechanical
• moving molecules collide with one another which
transfers energy between the two molecules
(kinetic)
• Energy sources can be converted from one form
to another
Metabolism and Biochemical Reactions
• All of the collective biochemical reactions of the body
are grouped into two general classes:
– Catabolic (exergonic) reactions
• decomposition reactions that release energy (due
to bonds breaking) in the form of HEAT into the
environment of the reaction
• reactants contain more energy than the products
– Anabolic (endergonic) reactions
• synthesis reactions that remove (store) energy
(HEAT) from the environment of the reaction to
create bonds
• products contain more energy than the reactants
• All reactions must overcome the activation energy
before the reaction takes place
– energy required to bring reactants together
Energy Flow in an Exergonic Reaction
Organic Molecules
• Molecules unique to living systems contain carbon and
are referred to as organic molecules
• Most of the anatomy and physiology of the body is
provided by the interaction between 4 different classes
of organic macromolecules
• Each class consists of small molecular subunits called
monomers (one unit)
– smallest subunits of macromolecules that exhibit
chemical properties of the macromolecule
• Monosaccharide (carbohydrates)
• Fatty acid (lipids)
• Amino acid (proteins)
• Nucleotide (nucleic acids)
– able to function individually or in covalently bound
groups
Biologically Important Organic Molecules
• Monosaccharides
– basic (smallest) unit of carbohydrates (sugars)
• Amino acids
– basic (smallest) unit of proteins
• Fatty acids
– basic (smallest) unit of lipids (fats)
• Nucleotides
– basic (smallest) unit of nucleic acids
Synthesis Reactions of Macromolecules
• Monomers can be covalently bound
to one another to create a molecule
gets progressively larger resulting
in a polymer (many units)
• Two or more small molecules
combine to form a larger one
• A+B  AB+C  ABC+D  ABCD…
Dehydration Synthesis
• 2 monomers are covalently bonded together to form a
a new molecule that is larger and structurally more
complex by the removal of a water molecule
(dehydration)
Decomposition Reactions
• Large polymer molecules can be
reduced down to the individual
monomers by breaking the covalent
bond between monomers through a
decomposition reaction
• ABC  AB+C  A+B+C
Hydrolysis
• Splitting a polymer by the addition of a water molecule
Exchange Reactions
• Two molecules collide and
exchange atoms or group of
atoms
• AB+CD  ABCD  AC + BD
Oxidation-Reduction (Redox) Reactions
• Involves the transfer of electrons from one
atom/molecule to another
– eg. formation of an ionic bond
• Reactants losing electrons are become oxidized (Loss
Electron(s) Oxidation = LEO)
• Reactants gaining electrons are become reduced
(Gain Electron(s) Reduction = GER)
• Na + Cl → Na+ + Cl– Na is oxidized and Cl is reduced
Reaction Rates
• The rate of chemical reactions are determined by
molecular motion and collisions between chemicals
• The speed at which a chemical reaction proceeds is
affected by:
– the concentration of reactants
• more concentrated = more collisions = faster rate
– the temperature
• higher temperature = faster molecular movement
= more collisions = faster rate
– the presence of catalysts
• “molecular matchmakers”
–bring reactants together faster
• biological catalysts are proteins called enzymes
Macromolecules
Carbohydrates
• “hydrated (H2O) carbon”
• Contain carbon, hydrogen, and oxygen
• Carbohydrate names end in the suffix “-ose”
– glucose, maltose, amylose, fructose, sucrose
• The monomer of carbohydrates is the
monosaccharide (one sugar) of which there are a
number of types
– glucose is the most biologically important
• Carbon:Hydrogen:Oxygen in a 1:2:1 atomic ratio
– glucose = C6H12O6
• Because they contain oxygen, they are polar
molecules (hydrophilic or lipophobic)
Monosaccharides
• Simplest molecular form of carbohydrates
• Three major monosaccharides
– obtained by the digestion (hydrolysis) of dietary
polysaccharides
– major function is to supply a source of cellular fuel
for the creation of chemical energy (adenosine
triphosphate ATP)
• Structural isomers (same formula (C6H12O6), different
structure
Disaccharides
• Pairs of monosaccharides covalently bonded together
• Three major disaccharides
– sucrose
• glucose + fructose
– lactose
• glucose + galactose
– maltose
• glucose + glucose
Polysaccharides
• Long chains of glucose form polysaccharides
• Starch (amylose)
– form of stored carbohydrates produced by plants
– the main source of dietary carbohydrates
– hydrolyzed to glucose molecules in the digestive
tract then distributed to all cells of the body
Polysaccharides
• Excess glucose in the body following the hydrolysis of
dietary carbohydrates is taken up by the liver and is
used to synthesize the polysaccharide glycogen
– the liver gradually hydrolyzes glycogen to glucose
between meals and releases it into the bloodstream
for distribution to all cells of the body
Lipids
• Nonpolar organic molecules made mostly of carbon
and hydrogen
• Energy rich molecules that can be used for energy
– typically occurs when there is an absence of usable
carbohydrates in the body
• Major molecule that provides structure to biological
membranes
• Used as signaling molecules for communication
between cells (steroid hormones)
Fatty Acids
• Hydrocarbon chains of 4 to 24 carbon atoms (always
an even number) bound to hydrogen atoms
• Has more energy per molecule than glucose
• 2 different functional groups are at each end
– carboxylic acid group
• provides acidic properties to the molecule
– methyl group
• 2 different types exist
– Saturated
• solid at room or body temperature (RT/BT)
– Unsaturated
• some are solid but most are liquid at RT/BT
Fatty Acids
• Hydrocarbon chains of 4 to 24 carbon atoms (always
an even number) bound to hydrogen atoms
• Has more energy per molecule than glucose
• 2 different functional groups are at each end
– carboxylic acid group
• provides acidic properties to the molecule
– methyl group
Fatty Acids
• 2 different types
– Saturated
• solid at room or body temperature (RT/BT)
– Unsaturated
• some are solid but most are liquid at RT/BT
• Saturated fatty acid
– each carbon in the hydrocarbon chain is saturated
with hydrogen (bonded to 2 hydrogens)
• no double bonds between carbons (C=C)
• Unsaturated fatty acid
– each carbon in the hydrocarbon chain is not
saturated with hydrogen
• contains at least one C=C
Types of Lipids
• The fatty acids (1, 2 or 3)
may be found in the body
bound to a molecule of
glycerol (glucose derived
molecule)
– monoglyceride
– diglyceride
– triglyceride
• Functions
– energy storage in adipose (fat) tissue
• each fatty acid of a triglyceride contains
approximately 4 times more energy than a single
molecule of a monosaccharide (glucose)
– insulation
• prevents excessive heat loss from the body
– protection
• provides shock absorption for organs that are
surrounded by adipose tissue
Phospholipids
• Similar in structure to a triglyceride consisting of:
– 1 glycerol
– 2 fatty acids
– 1 phosphate group (PO4-) with attached nitrogencontaining group
• Amphiphilic (both loving) molecule
– has BOTH polar and nonpolar portions
• Hydrophobic “tails” consist of two fatty acids
• Hydrophilic “head” consists of a negatively
charged phosphate and nitrogen-containing
groups
• Found in a liquid state at body temperature
• Predominant molecule in cellular membranes
Phospholipid Structure
Lipid Related Molecules
• The hydrocarbons in a
molecule of cholesterol
are arranged in a 4
ringed structure
• Cholesterol is used to
make steroid hormones
including:
– cortisol
– aldosterone
– estrogen
– testosterone
• Cholesterol is an
important component in
cellular membranes to
keep them in a fluid state
Proteins (Peptides)
• Polymer (chain) of amino acids which are bonded
together through covalent bonds called peptide bonds
• 20 different amino acids are used to create proteins by
the body
– 11 of the 20 amino acids (nonessential) can be
synthesized within the body and therefore do not
need to be supplied by the diet
– 9 of the 20 amino acids (essential) cannot by can
synthesized by the body and therefore need to be
obtained through hydrolysis of dietary proteins
during the digestive process
Amino Acids
• Each of the 20 different amino acids have similar
structural components
– a central carbon atom with an attached:
• an amino (NH2) group
• a carboxyl (COOH) group
• a hydrogen atom
• Each amino acid unique due to the functional group
located at the R position attached to the central
carbon atom
Amino Acids
• The 20 amino acids can also be divided into 2 groups
based on their solubility in water
• The molecular composition of the R group determines
whether an amino acid is
– polar
– nonpolar
• The polarity of amino acids play a crucial role in
determining the overall 3 dimensional structure of
proteins which in turn determines its biological function
Protein Structure
• The 20 different amino acids can be joined by peptide
bonds with an almost infinite number of combinations
• Proteins vary greatly in size
– some are as small as 3 amino acids in length
– some are as large as 34350 amino acids in length
• 4 levels of structural complexity in proteins
• Primary structure
– the amino acid sequence of the protein
– glutamic acid – histidine – proline is the amino acid
sequence of thyrotropic releasing hormone
– determined genetically and is required for proper
protein function
• a single amino acid deletion or substitution could
lead to a completely dysfunctional protein
– since each protein has a unique amino acid
sequence, each protein is structurally and
functionally unique
Protein Structure
• Secondary structure
– simple shapes that segments of amino acids make
within the protein
• α helix (coiled), β-pleated sheet (folded) shapes
are held together by intramolecular hydrogen
bonds between nearby amino acids
• Tertiary structure
– the overall 3 dimensional shape of the protein
– determined by polar and nonpolar interactions
between the amino acids of the protein and the
surrounding water
– stabilized by intramolecular hydrogen bonds and
disulfide bridges
• Quaternary structure
– two or more separate polypeptide chains interacting
with one another to create a functional unit
Protein Conformation and Denaturation
• Conformation
– overall 3 dimensional shape (tertiary/quaternary)
that is required for function (activity)
– the function of some proteins requires an ability to
change their conformation
• Denaturation
– drastic conformational change in a protein caused
by the breaking of hydrogen bonds within a protein
• increases in temperature
• increases or decreases in pH
– can be partial or complete
• when a protein is partially denatured, its function
is impaired
• when a protein is completely denatured, its
function is lost
Protein Types and Functions
PROTEINS PERFORM ALL BODY FUNCTIONS
Proteins are categorized into 2 groups
• Globular proteins are water soluble and function in:
– Catalysis
• enzymes speed up biochemical reactions
– Communication
• hormones and neurotransmitters act as signaling
molecules between cells
– Cell Membrane Transport
• channels allow substances to enter/exit cells
• Fibrous proteins are insoluble in water and function in:
– Structural integrity
• collagen and elastin hold body parts together
– Movement
• actin and myosin allow for muscle contraction
Characteristics of Enzymes
• Enzymes are chemically specific for a particular
substrate (chemical on which an enzyme acts upon)
– each enzyme can only act upon one substrate
• Enzymes are unchanged by reactions that they
catalyze and are able to repeat the process many
times over
• Enzymes increase the rate of a chemical reaction by
lowering the activation energy of the reaction
• Enzymes are frequently named for the type of reaction
they catalyze or by their substrate
• Enzyme names usually end in the suffix -ase
Enzymes and Activation Energy
Enzyme Structure and Action
• The region of an enzyme that recognizes a substrate
is called the active site
– recognizes the specific molecular structure of a
substrate
• An enzyme temporarily binds its substrate(s) and
allows the appropriate chemical reaction proceed
– Synthesis
– Decomposition
– Exchange
– RedOx
Enzymatic Catalysis of a Biochemical Reaction
Nucleic Acids
• Largest molecules in the body
• Molecules of instruction and heredity
• Two major classes
– deoxyribonucleic acid (DNA)
– ribonucleic acid (RNA)
• The monomers of nucleic acids are nucleotides
Nucleotides
• A nucleotide has 3 parts
– a nitrogen containing base (arranged in a ring(s))
– a sugar
– a phosphate group
• 5 different nucleotides are used to make nucleic acids
– Each nucleotide is different based on 2 criteria:
• the identity of the nitrogen base
–double ringed bases are called purines
• adenine (A) and guanine (G)
–single ringed bases are called pyrimidines
• cytosine (C), thymine (T) and uracil (U)
• the identity of the sugar (DNA uses deoxyribose
while RNA uses ribose)
• Nucleotides are covalently bound to one another
between the sugar of one nucleotide and the
phosphate of another nucleotide to make long straight
(linear) molecules referred to as nucleic acid strands
Nucleotides
DNA
• Double-stranded helical molecule
– looks like a ladder that has been twisted
– each strand is between 100 million to 1 billion
nucleotides in length
– 2 strands are held together by H-bonds between
complimentary nucleotides on opposite strands
• H-bonds can only be made between a purine on
one strand and a pyramidine on the other strand
–A can only bind with T
–G can only bind with C
–U is NOT part of DNA (only found in RNA)
• The sequence of nucleotides in one of the strands
contains the genetic code
• the amino acid sequence of all proteins
Structure of DNA
RNA
• Single-stranded molecule
– made from the nucleotides A, U, G and C
• Three varieties of RNA:
– messenger RNA
– transfer RNA
– ribosomal RNA
Adenosine Triphosphate (ATP)
• Source of immediately usable energy for the cell
• Nucleotide derivative bound to 3 phosphate groups
– second and third phosphate groups are attached by
high energy covalent bonds
• phosphate groups are negatively charged and
naturally repel each other
• Enzymes that hydrolyze the high energy bond of ATP
produces releases chemical energy
– ATP → ADP + P + energy
• the body can convert the ADP and P back into
ATP using the energy stored in the covalent
bonds of carbohydrates and lipids as a fuel
ATP