Biomolecules
Atoms
•
Atoms have 3 components: protons, neutrons, and
electrons
– The type of element (carbon, iron, etc. ) is entirely
determined by how many protons are in the nucleus.
•
protons and neutrons are in the nucleus
– Protons have a +1 charge
– Neutrons have no charge
•
Electrons circle around the nucleus, in a series of
shells.
– Electrons have a -1 charge
– Chemical bonds are created by movements of the
electrons between atoms
•
The number of protons determines which element
the atom is.
– Hydrogen: 1 proton, carbon = 6 protons, oxygen = 8
protons.
– Biological and chemical processes never change the
number of protons in any atom.
•
Normally, the number of electrons is equal to the
number of protons, so the atom has no electrical
charge: it is neutral.
Covalent Bonds
•
Covalent bonds occur when 2 atoms
share a pair of electrons. The
electrons spend part of their time
with both atoms.
•
A molecule of hydrogen gas, H2, has 2
hydrogen atoms. Each atom provides
1 electron, so in the bond each atom
shares 2.
•
The bond is symbolized as a line
connecting the 2 H’s: H-H
↑ In water (H2O), the oxygen has 6
electrons in its outer shell, and it
shares one with each of the 2
hydrogens, giving 8 shared electrons
for oxygen and 2 for each hydrogen.
•
Each element has a characteristic
number of bonds it forms: carbon =
4, nitrogen = 3, oxygen = 2, hydrogen
= 1.
Polar Covalent Bonds
•
Sometimes the electrons in a covalent bond
aren’t shared equally, because one atom
attracts electrons more strongly than the other.
When this happens, the electrons spend more
time with one atom, and that atom becomes
slightly negatively charged. The other atom
becomes slightly positively charged. This is a
polar covalent bond, because the atoms form
positive and negative poles.
– Bonds where the electrons are shared
equally are called non-polar.
•
Water is a polar compound, because the oxygen
is slightly negative and the hydrogens slightly
positive.
– Oxygen attracts electrons more than
hydrogen
Polar molecules attract each other: the opposite
charges attract.
•
Water
• Water forms many hydrogen bonds with
other water molecules and with other
polar substances. This causes water
molecules to stick together (causing
surface tension) and stick to other things
(causing capillary action, how water gets
from the roots to the top of trees).
• Polar substances dissolve in water,
because water forms hydrogen bonds
with the polar molecules. Thus, polar
substances are called hydrophilic, or
“water-loving”.
• Non-polar substances don’t dissolve in
water because they can’t form hydrogen
bonds, so they are called hydrophobic, or
‘water-fearing”. Oils and fats are
examples of non-polar substances.
• Soap works by having a non-polar end,
which dissolves in grease, and a polar
end, which dissolves in water. Soap
causes tiny droplets of grease to be
suspended in water, where they can be
rinsed away.
Organic Compounds
• It used to be thought that only living
things could synthesize the
complicated carbon compounds
found in cells
• German chemists in the 1800’s
learned how to do this in the lab,
showing that “organic” compounds
can be created by non-organic
means.
– Raw materials: coal and oil
• Organic compounds are those that
contain carbon. (with a few
exceptions such as carbon dioxide
and diamonds)
Four Basic Types of Macromolecule
• Most organic molecules in the cell are long chains of similar subunits.
Because they are large, these molecules are called macromolecules.
Each macromolecule has a different type of subunit.
• The four types of macromolecule are:
1.
2.
3.
4.
carbohydrates (sugars and starches), Subunit = simple sugar.
lipids (fats). Subunits = fatty acids and glycerol
proteins, Subunits = amino acids
nucleic acids (DNA and RNA). Subunits = nucleotides
• The cell also contains water, inorganic salts and ions, and other small
organic molecules.
• Plants often produce secondary metabolites: special compounds that
attract pollinators, inhibit microorganisms, deter grazing animals, etc.
We have found uses for many of these secondary metabolites as
medicines, spices, and drugs.
Carbohydrates
• Sugars and starches: “saccharides”.
• The name “carbohydrate” comes from
the approximate composition: a ratio of
1 carbon to 2 hydrogens to one oxygen
(CH2O). For instance the sugar glucose
is C6H12O6.
• Carbohydrates are composed of rings of
5 or 6 carbons, with –OH groups
attached. This makes most
carbohydrates water-soluble.
• Carbohydrates are used for energy
production and storage (sugar and
starch), and for structure (cellulose).
Sugars
• Monosaccharides, or simple sugars, like glucose
and fructose, are composed of a single ring.
• Glucose is the primary food molecule used by
most living things: other molecules are converted
to glucose before being used to generate energy.
Glucose can also be assembled into starch and
cellulose.
– Fructose is a another simple sugar found in plants,
It is sweeter than glucose and is used to sweeten
may food products.
• Disaccharides are two simple sugars joined
together. Most of the sweet things we eat are
disaccharides: table sugar is sucrose, glucose
joined to fructose. Plants use photosynthesis to
make glucose, but convert it to sucrose for ease
of transport.
– Maltose, malt sugar, consists of two glucoses
joined together. It is a breakdown product of
starch, which yeast converts to ethanol when
beer is brewed.
Complex Carbohydrates
• = polysaccharides (many sugars linked
together).
– Can be linear chains or branched.
• Some polysaccharides are used for food
storage: starch.
– Starch is a glucose polymer, we have
enzymes that easily digest starch.
– Starch is a convenient way to store
glucose in both plants and animals.
• Some polysaccharides are structural: the
cellulose of plant cell walls and fibers is
a polysaccharide composed of many
glucose molecules, but linked together
differently than starch.
– We don’t have enzymes that can digest
these polymers. Cows and termites
depend on bacteria in their guts to
digest cellulose, producing methane as a
byproduct.
Lipids
• Lipids are the main non-polar component
(hydrophobic) of cells. Mostly hydrocarbons—
carbon and hydrogen.
• They are used primarily as energy storage and
cell membranes.
• 4 main types: fats (energy storage),
phospholipids (cell membranes), waxes
(waterproofing), and steroids (hormones).
• Waxes: waterproof coating on plants and
animals. Composed of fatty acids attached to
long chain alcohols.
– The ability of plant to coat themselves in waxes
was crucial to the ability to live on dry land.
• Steroids have carbon atoms arranged in a set
of 4 linked rings.
– Cholesterol is steroid; it is an essential
component of cell membranes (along with the
phospholipids).
– Many human hormones are steroids
Triglycerides and Phospholipids
• Triglycerides are the main type of
fat. A triglyceride is composed of 3
fatty acids attached to a molecule of
glycerol.
– Fatty acids are long hydrocarbon
chains with an acid group at one
end.
• Fats store about twice as much
energy per weight as carbohydrates
like starch.
• Phospholipids are the main
component of cell membranes.
– they have a glycerol with 2 fatty acids
attached, plus a phosphate-containing
“head” group instead of a third fatty acid.
• The head group is hydrophilic, while
the fatty acids are hydrophobic.
• Cell membranes are 2 layers, with
the head groups facing out and the
fatty acids forming the interior of
the membrane.
Proteins
• The most important type of
macromolecule. Roles:
– Enzymes: all chemical reactions in the
cellsare catalyzed by enzymes, which are
proteins: building up, rearranging, and
breaking down of organic compounds,,
generating energy
– Structure: collagen in skin, keratin in hair,
crystallin in eye. Also, movement of
materials inside the cell.
– Transport: everything that goes in or out of
a cell (except water and a few gasses) is
carried by proteins.
• All organisms contain protein, but
animals have much more protein than
plants: most of the animal body is
composed of protein, while most of
the plant body is carbohydrate.
– Proteins are 1/3 nitrogen. Acquiring
this nitrogen and getting rid of
nitrogenous waste is a big problem
animals face.
Amino Acids
•
•
•
•
•
Amino Acids are the subunits of
proteins.
Each amino acid contains an amino
group (-NH2) and an acid group
(COOH). Proteins consist of long
chains of amino acids, with the acid
group of one bonded to the amino
group of the next.
There are 20 different kinds of amino
acids in proteins. Each one has a
functional group (the “R group”)
attached to it.
Different R groups give the 20 amino
acids different properties, such as
charged (+ or -), polar, hydrophobic,
etc.
The different properties of a protein
come from the arrangement of the
amino acids.
Protein Structure
• A polypeptide is one linear chain of amino
acids. A protein consists of one or more
polypeptides, and they sometimes contain
small helper molecules such as heme.
– Many co-factors are vitamins: molecules
our body can’t make for itself, so we have to
get from our food.
• After the polypeptides are synthesized by
the cell, they spontaneously fold up into a
characteristic conformation which allows
them to be active. The proper shape is
essential for active proteins. For most
proteins, the amino acids sequence itself is
all that is needed to get proper folding.
– The joining of polypeptide subunits into a
single protein also happens spontaneously,
for the same reasons.
• Denaturation is the destruction of the 3dimensional shape of the protein. This
inactivates the protein, and makes it easier
to destroy. Heat is the easiest way to
denature proteins: this is the effect of
cooking foods.
Nucleic Acids
•
•
•
•
•
•
Nucleotides are the subunits of nucleic
acids.
Nucleic acids store and transmit genetic
information in the cell.
The two types of nucleic acid are RNA
(ribonucleic acid) and DNA
(deoxyribonucleic acid).
Each nucleotide has 3 parts: a sugar, a
phosphate, and a base.
The sugar, ribose in RNA and
deoxyribose in DNA, contain 5 carbons.
They differ only in that an –OH group in
ribose is replaced by a –H in DNA.
The main energy-carrying molecule in
the cell is ATP. ATP is an RNA nucleotide
with 3 phosphate groups attached to it
in a chain. The energy is stored because
the phosphates each have a negative
charge. These charges repel each other,
but they are forced to stay together by
the covalent bonds.
DNA and RNA
• DNA uses 4 different bases: adenine
(A), guanine (G), thymine (T), and
cytosine (C). The order of these bases
in a chain of DNA determines the
genetic information.
• DNA consists of 2 complementary
chains twisted into a double helix and
held together by hydrogen bonds.
DNA is a stable molecule which can
survive thousands of years under
proper conditions
– The DNA bases pair with each other:
A with T, and G with C.
• RNA consists of a single chain that
also uses 4 bases: however, the
thymine in DNA is replaced by uracil
(U) in RNA. RNA is much less stable
than DNA: it is used to convey
information for immediate use by the
cell.
Human Nutrition
• To make all those molecules, we need various raw materials. The
absence of any essential nutrient leads to disease and death.
• Sufficient food molecules to supply our energy needs: calories.
These can be carbohydrate, protein, or fat.
– Fat has about twice the calories pr weight as carbohydrates or protein.
– Protein generates ammonia waste (urine).
• Some amino acids and fatty acids we can’t make for ourselves
– Amino acids: 10 of the 20 are required in the diet.
– Fatty acids: omega-3 (linolenic acid) and omega-6 (linoleic acid) fatty
acids are required.
• Small amounts of small complex molecules used by enzymes to
catalyze chemical reactions. There are 15 known vitamins.
• Elements in a usable form: these are called minerals: phosphorus,
calcium, iron, zinc, magnesium, manganese, a total of 17 elements,
not including carbon, hydrogen, oxygen, and nitrogen.
Some Deficiency Diseases
• Undernutrition: not enough calories. Mostly in young children, and mostly
they die of other diseases that would be easily overcome by the wellnourished.
• Protein deficiency diseases. Some get sufficient calories (as form a starchy
diet) but not enough complete protein: some essential amino acids are
insufficient.
• Vitamin deficiencies:
– Vitamin A. Used in visual pigment and in skin. Permanent blindness can result
from deficiency. Made from carotene.
– Vitamin C. Needed to make collagen in skin. Scurvy.
– Vitamin D. Used as a hormone that regulates calcium levels in the body.
Deficiency leads to rickets: malformed bones, especially legs. Precursor made
in liver, then transported to skin so UV can convert it to active form. Darker
skinned people need more sunlight than lighter skinned
• Thiamine. Used in breakdown of carbohydrates. Beriberi, seen in people who
live on polished rice. Japanese sailors in 1880’s. Brown rice cures it.
Some Deficiency Diseases
• More vitamins:
– Niacin. Used in electron transport, essential for energy generation. Can be
made from the amino acid tryptophan, which is lacking in maize. Pellagra
leads to insanity: in the early 20th century, half the patients in mental hospitals
in the US South had pellagra.
• Vitamin B12 (cobalamin). Only bacteria make it. Plants don’t use it or contain
it. Herbivores get it from their gut bacteria, and we get it by eating meat and
dairy products. Pernicious anemia.
– Minerals:
•
•
•
•
Sodium. Plants have very little of it. It has been a valuable commodity: salt
mines.
Calcium. Used in many places, especially muscle and bone. Osteoporosis.
Iron. Needed for hemoglobin in the blood. Iron deficiency anemia is the most
common form of nutrient deficiency. Rather hard to absorb.
Iodine. Part of thyroid hormone. Not used in plants, but lots in the sea, so
seaweed and other marine things have a lot of it. Goiter: swollen thyroid
glands, used to be common in the Midwest, but now we use iodized salt.