Biology Molecule Essay, Research Paper
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