Biology Molecule


     Unit 1 -man is high 50ís to 60% water -distribution in body divided into 3
compartments: 1) intracellular - 28 litres 2) intercellular/interstitial fluid -

11 litres - 80% 3) blood plasma - 3 litres - 20% -women contain less water than
men -organisms can contain 60-80% water -bacteria have lots of water -fat cells
have little -waterís properties result from its structure and molecular
interactions -water is polar -polar covalent bonds and asymmetrical shape give
it opposite charges on opposite sides -electrons spend more time around O giving

H a slight positive charge -hydrogen bonds form between the oxygen of one
molecule and the hydrogen of another -cohesion: substance being held together by
hydrogen bonds -hydrogen bonds are transient yet enough is always held together
to give water more structure than almost any other liquid -beads and meniscus
formed by cohesion (also helps upward transport of water in plants) -adhesion
counteracts downward pull of gravity -water has greater surface tension than
most liquids -surface molecules are hydrogen bonded to molecules below and
around them -surface tension can hinder life (i.e. beading in the alveoli of
lungs) -makes water "unwettable" -surfactants used to counteract this -water
has a high specific heat which allows it to resist extreme temperature changes
-has a high heat of vaporization that causes it to require alot of energy to
change states -when sweating, heat energy is utilized to change states from
liquid to gas, causing a drop in temperature -as a solid water is less dense
than as a liquid and will float -charged regions of molecules have an electrical
attraction to charged ions -water surrounds ions separating and shielding them
from one another -polar compounds are generally soluble -charged regions of
water are attracted to oppositely charged regions of other polar molecules
-polar molecules are miscible in other polar liquids -most water molecules
donít dissociate (~ 1/554 million do) -hydrogen atom in hydrogen bond between
the two water molecules may shift from the oxygen atom it is covalently bonded
to the unshared orbitals of the oxygen that it is hydrogen bonded to -hydrogen
ion is transferred creating a hydronium ion and leaving a hydroxide ion -the
solvent is water itself -at equilibrium water is not dissociated -at equilibrium
in pure water at 25oC [H+] = [OH-] -pH of this solution is 7 (neutral) -high pH
= low acidity -acids are substances that increase the relative [H+] and remove

OH- because it tends to combine with H+ to form water - if [H+] * [OH-] , it is
acidic and has a pH between 0 and 7 -bases are substances that reduce the
relative [H+] in a solution -it may increase the [OH] -if [H+] * [OH-] , it is
basic and has a pH greater than 7 -buffers are important in the body to keep the
pH range between 6 and 8 -pH of blood is between 7.34 and 7.44 -mustnít shift
below 7.2 or acidosis will occur -some body zones may have a pH as low as 0.5 or
as high as 10 -buffers minimize sudden changes and are a combo of hydrogen
donors and hydrogen acceptors -ions are accepted when in excess and donated when
in short supply -in biological systems an example is the bicarbonate buffer -in
response to a rise in pH, the carbonic acid dissociates to form a carbonate ion
and a hydrogen proton -if there is a drop, it is reversed (pH up = to right, pH
down = to left) -equilibrium is established but it is always moving to the left
or the right -a balance is the optimum pH -other body buffers include protein
molecules which donate and accept amino acids to stabilize pH -most of the rest
of organisms is made up of carbon based compounds like carbs, lipids, proteins,
nucleic acids -carbon compounds are known as organic -vitalism is the belief in
a life force outside the control of chemical laws -this has been disproved as
water, ammonia, hydrogen and methane have been combined in a lab to form organic
substances -C+O+H = carbohydrates -C+H+N = amino acids, urea, proteins, lipids
-carbon atoms are the most versatile building blocks -each has 4 valences where
bonds can form -carbon chains form the skeleton of most organic molecules -may
be straight or branched, long or short, or in closed rings -hydrocarbons contain
only hydrogen and carbon -they form when organic matter decomposes and
functional groups break off leaving a skeleton -hydrocarbon chains, branches,
and rings can be modified by other elements which are joined on in a particular
matter -these are components of organic molecules that are often involved in
chemical reactions -they replace 1 or more hydrogens in a hydrocarbon

Carbohydrates: -sugars and starches -nonsugars: plant starch, animal starch,
cellulose, chitin -come from pasta, rice, flour, fruit, syrups -important source
of energy, can be oxidized to release energy, improves your mood -contain C, H,
and O, with generally 2 times as much H as O -sugar names usually end with -ose,
and are named depending on the number of carbons in them (e.g. triose, pentose)
-6 carbon sugars, hexoses, are most important -general formula is C6H12O6, and
in living systems, the state is aqueous -solids exist in chains, and liquids as
rings -the molecular formula is the same for different hexoses, but the
structural formula differs -other isomers of glucose can be reorganized by cells
into alpha glucose, and then oxidized -glucose is the major nutrient for cells
and its carbon skeleton is raw material for the synthesis of other organics

Disaccharides: -2 hexose sugars-most common are: sucrose, lactose and maltose
-glucose + glucose = maltose + water -glucose + fructose = sucrose + water
-glucose + galactose = lactose + water -this process is known as condensation or
dehydration synthesis -synthesis of disaccharides doesnít happen in the human
body, but usually they are eaten and digested, through a process known as
hydrolysis or disaccharidases Polysaccharides: -these are macromolecules that
are made by condensation when monosaccharides are joined -general molecular
formula isC6H12O5 -common polysaccharides are amylose, amylopectin (plant
starch), glycogen (animal starch), cellulose (cell wall material), chitin
(leathery covering of invertebrates) -plants use glucose to grow, and extra is
stored in the roots in a soluble form which is then reactivated in the spring -
this reactivates the growing process year after year -animal starch is stored in
special cells (average person has a 24 hour supply) and can readily be converted
into glucose for use -cellulose and chitin are structural carbohydrates -amylose
is formed when glucose molecules join in a 1-4 linkage pattern -first carbon of
one glucose links to the fourth carbon of another -this is a covalent bond or a
glycosiolic link -bond is angular and forms a spiral called an alpha helix -if
it branches, amylopectin is formed -cellulose is a 1-4 linkage of beta glucose
-this creates a straight strand and not a helix -these bonds are rigid and
require special enzymes (cellulase) to break them -the position of the beta
glucose molecules alternates Lipids: -humans rarely eat pure lipids -cell
membranes are primarily lipid and lipids can easily enter cells, carrying a
foodís flavor with them -a diet should have less than 30% fat, 55-65% carbs,
and 10-15% protein -lipids are important as a source of energy, insulation
(adipose tissue), cushions for the internal organs, as a lubricant, as an
emulsifying agent (cholesterol in bile), as a structural component of cells (1/6
of brain is fat), cholesterol as a precursor molecule for vitamin D, cortisone,
testosterone, progesterone, and estrogen -lipids are simplest biological
molecules and are composed mostly of C, H and a few Os -they are energy rich
because of the high C to H ratio -fat consists of a glycerol molecule connected
by ester bonds to a 3 fatty acid molecule (this is a tryglyceride) -if the bonds
between the carbons are single bonds, the fatty acid is saturated (fat formed is
a saturate) -if they have multiple bonds, it is an unsaturated fat -a
polysaturate is more than one fatty acid held together by single bonds -multiple
bonds can be broken and extra hydrogens added through hydrogenation -short
chained fats of unsaturated fatty acids are soft with a low b.p. -long chained
fats of saturated fatty acids are harder with a high b.p. -length of chains
affects boiling point the most -to make an oil from a solid, you must
hydrogenate it Steroids: -saturated fatty acids can be converted to the steroid
cholesterol -triglycerides are monitored more closely in the blood than
cholesterol -the amount of saturates converted to cholesterol is genetic
-abnormal genes can cause excessive production (1 gene = severe heart disease, 2
= shortened life span) -liver produces cholesterol -steroids have a 5 ring shape
-examples are androgens, estrogens, and cortisone Proteins: -there are 20 amino
acids, 8 of which are essential and can be converted into any of the other 12
-protein rich foods are digested into amino acids and the body absorbs them to
make their own proteins -liver cells convert them into absent aminos =
transaminofication -proteins are synthesized on ribosomes in the cytoplasms of
cells or on polysomes (ribosome chains0 -DNA codes proteins by copying its info
onto a shorter strand known as mRNA (m = a message to synthesize a protein) -the
message is received and a protein is synthesized -for synthesis all 20 are
required -number, sequence and type of amino acids making up the protein is the
primary structure - this is determined by DNA -secondary structure is the
coiling or pleating of amino acid chains, caused by rigid peptide bonds which
are bent by strong intermolecular attraction between hydrogens and oxygens of
every fourth amino - this results in a regular, repeating twist or an alphahelix
-chains lie parallel to one another and form hydrogen bonds between themselves -
this is a beta sheet but is not very common -secondary structure is determined
by intermolecular bonds -tertiary structure refers to the folds in the coiled
chain -this is called by a thiol called cysteine - this can form a bridge when
it meets another cysteine -when 2 cysteines meet, a disulfide link is formed
-insulin has 6 cysteine amino acids and forms 3 bridges and a slightly globular
protein -the more cysteine amino acids there are, the more folds or joints that
result and the more globular the protein is -globular proteins are the"doers" that function because they have a particular shape due to the
cysteine-cysteine sulfur bridges -some proteins may be a bunch of polypeptide
chains close together -this is quaternary structure, which very few proteins
have -all proteins have a primary and secondary structure, but few have a
tertiary structure, and even fewer a quaternary -proteins can be 50-50,000 amino
acids long -amino acids are joined by peptide bonds, a covalent bond between the

C of one amino acid and the N of a neighbour -a polypeptide chain is a string of
aminos not long enough to be a protein -amino acids are so named because of
their two functional groups, the amine group and the carboxylic acid group

Nucleic Acids: -all living cells contain DNA and RNA -these carry instructions
for making proteins and specify the sequence in which amino acids should be
linked together -DNA and RNA are polynucleotides, polymers of nucleotides
-nucleotides consist of a phosphate group + a pentose + a nitrogenous base -they
can be linked together by condensation to form a polynucleotide -if a nucleotide
contains ribose, it becomes Ribo Nucleic Acid -these are always just a single
strand, but may be looped into 3 dimensional shapes -if the nucleotide contains
deoxyribose, Deoxyribo Nucleic Acid results -DNA molecules are far longer than

RNA molecules, and can never contain Uracil -4 possible bases are adenine,
guanine, cytosine, and thymine -DNA molecules contain two polynucleotide
strands, held together by hydrogen bonds between the bases -hydrogen bonds can
only be formed between specific base pairs: Adenine - Thymine Cytosine - Guanine
-a sense strand is a sequence of bases that tells the order in which to string
together the amino acids -a length of DNA coding the sequence for a polypeptide
is called a gene -three bases, a codon, specify an amino acid -there are 64
possible arrangements of bases in a codon -polypeptides are made when 2 strands
of DNA split up and an RNA molecule builds up against the sense strand -base
sequence of RNA must match that of the DNA molecule -a complete RNA molecule
then peels off and travels to the location where polypeptides are made -sequence
of bases on a DNA molecule is the same for a human or a bacteria Other

Nucleotides: -a slightly different version of one of the nucleotides that forms

RNA is ATP -ATP contains ribose, adenine and 3 phosphate groups instead of 1
-phosphate groups may be lost one at a time to make ADP (di) or AMP (mono) -all
living cells make ATP as an energy currency, it is produced constantly -ATP
molecules usually last less than a minute before being broken down -~40 kg is
produced in a day -if a cell needs energy, it hydrolyses ATP and releases energy
in small packets NAD: -contains ribose sugar, adenine and 2 nucleotides -one
nucleotide does not contain any of the 5 bases, but instead a nicotinamide ring
-they can accept hydrogens and become NADH -hydrogens are accepted or passed on
during respiration or photosynthesis.