Biology Molecule
Unit 1 -man is high 50’s 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
-water’s 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
don’t 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 -mustn’t 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 doesn’t 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
food’s 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.