Download 3 Chemistry

CHEMISTRY
Levels of Structural Organization
 Chemical – atoms combined to form molecules
 Cellular–cells are made of molecules
 Tissue – consists of similar types of cells
 Organ – made up of different types of tissues
 Organ system – consists of different organs that work closely together
 Organismal – made up of the organ systems
Composition of the body:
 Major elements: (96%) – Carbon (C ), Oxygen (O), Nitrogen (N), Hydrogen (H)
 Lesser elements make up 3.9% of the body and include:
– Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na),
Chlorine (Cl), Magnesium (Mg), Iodine (I), and Iron (Fe)
 Trace elements make up less than 0.01 % of the body – They are required in
minute amounts, and are found as part of enzymes
 Elements combine to make molecules
–H2O –CO2– O2
Chemistry Overview
 Atoms
o Nucleus with protons, neutrons, electrons
o Ions
 Bonding
o Covalent bonds
o Ionic bonds
o Hydrogen bonds
Atoms
 All matter is composed of elements, which cannot be broken down into simpler
substances by ordinary methods.
 Carbon, oxygen, hydrogen, and nitrogen make up about 96% of our body weight.
 Each element is composed of atoms.
 Atoms are a cluster of particles called protons, neutrons, and electrons.
 The protons (+ charge) and neutrons (no charge) make up the center of the atom
(its nucleus), and the electrons ( - charge) circle the nucleus of the atom in an
orbital motion.
Elements
 What makes one element different from another element is the number of
electrons orbiting the nucleus of the atom.
 Hydrogen has only one electron.
 Oxygen has eight electrons.
 The first two electrons of any atom always orbit at the closest distance to the
nucleus, called the first valence shell.
 The next largest shell around the nucleus can hold up to 8 electrons. If there are
more electrons than that, they will orbit in the next shell, and so on.
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Oxygen
 Since Oxygen has 8 electrons, the first two stay in the inner orbital. The next 6
will stay in the next largest orbital. Since that orbital can hold 8, oxygen always
seeks two more electrons to complete its outermost shell (all the other elements
do this also).
 Therefore, oxygen frequently pairs with itself and shares its electrons. The first
oxygen uses two electrons from the other oxygen, while the other does likewise.
Thus, they often travel in pairs, called O2.
An element is an atom with a certain number of electrons (electrical charges) circling
around it in an orbit.
What would happen if oxygen were to disappear worldwide for five seconds?
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Water
 Since hydrogen has one electron, it needs one more to complete its outermost
orbital.
 It frequently binds with another hydrogen and one oxygen (H2O). Both hydrogens
donate their electron to the one oxygen so the oxygen can have its outer electron
orbital filled, and both hydrogens have their outer orbitals filled also.
 The bond form by hydrogen and water is a covalent bond, which is strong.
 The water molecule then has a positive charge on one end and a negative charge
on the other end.
 The positive charge on one water molecule will be attracted to the negative charge
on a different water molecule. This bond is a hydrogen bond, which is weak and
easily broken.
 Ice is less dense than liquid water
o Hydrogen bonds hold molecules in ice farther apart than in liquid water
Compounds
 Two or more elements
 Hydrogen (H) and Oxygen (O) = H2O
 Sodium (Na) and Chlorine (Cl) = NaCl
 Demonstrates new properties with a higher level of structural organization
 Carbon, hydrogen, oxygen, and nitrogen form most of the compounds in living
organisms
 Elements can combine to form compounds
o Sodium and chloride ions
 Bond to form sodium chloride, common table salt
Water is the solvent of life
 Solution: a liquid consisting of a uniform mixture of two or more substances.
 Solvent: the dissolving agent
 Solute: the substance that is dissolved
Ions
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An ion is an atom or molecule in which the total number of electrons is not equal
to the total number of protons, giving it a net positive or negative electrical
charge.
Sodium = Na+
Potassium = K+
Chloride = Cl-
Types of Chemical Bonds
 Covalent bond: two atoms sharing elections; stable.
 Hydrogen bond: when hydrogen, having a positive charge (it lacks an electron)
is attracted to an atom with a negative charge. In this case, the electrons are not
shared; the bond is electromagnetic. These bonds are weak and unstable. This
type of bond pulls a protein into its 3-Dimensional shape. Acids and heat can
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break the bond, causing the protein to straighten out. Hydrogen bonds also cause
curly hair. A hot iron can break the bonds and the hair will straighten or curl in
the position it cools in. Getting the hair wet will reform the hydrogen bond and
the hair goes back to its original position.
Ionic bond: Formed through an electrostatic attraction between two oppositely
charged ions. Ionic bonds are formed between a cation (+), which is usually a
metal, and an anion (-), which is usually a nonmetal. Sodium and fluorine bonding
ionically to form sodium fluoride. Sodium loses its outer electron to give it a
stable electron configuration, and this electron enters the fluorine atom
exothermically. The oppositely charged ions are then attracted to each other.
Acids and Bases
 Some water molecules break apart into ions.
o Hydrogen ions (H+)
o Hydroxide ions (OH-)
 Acid: excess hydrogen ions (H+)
o hydrochloric acid in your stomach
 Base: excess hydroxide ions (OH-)
o Ammonia is a base
pH scale
 Neutral: pH = 7
 Acid: pH < 7
 Base: pH > 7
Macromolecules: The molecules of Life
96% of the human body is composed of just four elements. They are carbon, hydrogen,
oxygen, and nitrogen. These elements combine to larger units called molecules. There are
two types of molecules in our bodies; organic and inorganic.
INORGANIC MOLECULES are not made of carbon atoms.
1. SALTS are found in body fluids. They are needed for muscle contraction
and nerve conduction.
2. WATER
The body is about 70% water. All of our body’s chemical reactions require it.
It keeps the body from overheating
It also prevents drastic changes in temperature.
One spring, a baby finch collapsed with exhaustion on my patio. Since it was exhausted,
it probably wasn’t good at finding food and water yet. That means it was dehydrated and
hungry. I knew to get an eyedropper and give it water with sugar in it because those are
the two main things it needs right away. We discussed water, now let’s get to sugars.
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ORGANIC MOLECULES are made of carbon, which is what our body is mostly
made of. The three main types of organic molecules in our body are carbohydrates,
lipids, and proteins.
1. Carbohydrates (built from simple sugars)
2. Lipids (built from fatty acids)
3. Protein (built from amino acids)
Nucleic acids (built from nucleotides)
1. CARBOHYDRATES are molecules that store energy a short time,
compared to lipids.
a) SIMPLE CARBOHYDRATES (known as sugars), such as those
found in candy. They are used for a quick source of energy, and they are burned off fast.
The main sugar form is glucose.
b) COMPLEX CARBOHYDRATES (known as starch) is a storage form
of glucose in plants. There is a lot of starch in flour and potatoes. When we eat breads
and potatoes, we convert the starch to glucose. Starch does not break down into glucose
easily (it takes energy), so they tend to get stored and are only broken down when there is
not enough glucose available.
c) CELLULOSE is only found in plant cell walls, and gives plant stems
and leaves their firmness. Our body is unable to break down this substance, so it just
passes through our digestive tract. That is what is referred to as eating fiber. It helps a
person who has constipation. You may have heard the term cellulite referring to fat.
Don’t confuse cellulite with cellulose.
Simple Carbohydrates (sugars)
 Monosaccharides (single sugar)
 Disaccharides (two sugars linked together)
 Polysaccharides (more than two sugars linked together)
Monosaccharides (single sugar)
 Contain carbon, hydrogen, and oxygen (water around the carbon)
 Their major function - source of cellular energy(used in metabolism)
 also used to build more complicated molecules
Disaccharides or double sugars (also used as energy or food for cells)
Polysaccharides are polymers (chains) of simple Sugars
- uses:
– energy storage in cells
– attached to cell surfaces
Plants store starch
Animals store glycogen
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2. LIPIDS differ from carbohydrates in that they don’t dissolve in water.
a) FATS AND OILS: Fats are animal lipids, and oils are plant lipids.
When we ingest (eat) oils, we convert them to fats.
Function of fats
Fats are for long-term energy storage.
They also insulate against heat loss
Fat forms protective cushions around organs.
1) SATURATED FATTY ACIDS are solid at room temperature, like butter
and lard.
2) UNSATURATED FATTY ACIDS are liquid at room temperature, such as
vegetable oils.
b) STEROIDS are lipids that have a very different structure than fats. Steroids are
formed from cholesterol, which is found in the cell membranes of our body. An
example of steroids that our body makes is estrogen and testosterone.
Lipids: built from fatty acids
 Contain C, H, and a little O
 Greasy, oily, waxy molecules
 Examples of fats and oils:
- cholesterol
– triglycerides (adipose)
– Phospholipids (cell membranes, communication)
– Ear wax (protection)
– Skin oils (lubrication)
– Fat-soluble vitamins (vitamins A, D, E, K)
Adipose (Triglycerides)
 Composed of three fatty acids bonded to a glycerol molecule
 Used to STORE energy (fat)
Phospholipids
 Two fatty acid groups (“tails”) and a phosphorus group (“head”)
 Main use- major component of cell membranes
Lipids made from one fatty acid
 Cholesterol- all animal cells have this in the membrane
 Steroids –modified cholesterol- estrogen, progesterone, testosterone (hormones)
3. PROTEINS are molecules that make up most of our body. Our hair, nails, tissues,
ligaments, cartilage, bone, tendons, muscles, and organs are made of proteins. Other
proteins we have are enzymes, which function to break down larger molecules into
smaller ones. In order to understand what a protein is, we have to talk about amino acids.
a) AMINO ACIDS
b) NUCLEIC ACIDS
c) ATP
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Amino Acids build proteins
 Building blocks of protein, containing an amino group and a carboxyl group
 Amino acid structure: central C; amino group, acid group, and variable
group
a) AMINO ACIDS are monomers (building blocks) of protein. They are tiny carbon
molecules, made of just a carbon atom and a few other atoms. There are only 22 standard
types of amino acids in the human body (20 of them are involved in making proteins).
Nine of these are essential amino acids, meaning that we have to get them in the diet. We
can synthesize the others. Amino acids are like beads on a necklace. How they are
arranged on the string determines the type of necklace. Each bead is an amino acid, and
the whole necklace is the protein. A bunch of the same types of necklaces (proteins)
woven together makes up our tissues.
Proteins have two main shapes: Fibrous and Globular
 Fibrous proteins (rods)
– String-like proteins
– Examples: keratin, elastin, collagen, and certain contractile fibers found in muscles
 Globular proteins (rounded)
– Compact, spherical proteins
– Examples: antibodies, non-steroid hormones, and enzymes; hemoglobin (oxygen carrier
in the blood)
Properties of proteins in our body
 Proteins do basically all the work Many shapes and functions
– Surfaces of cells (communication, recognition, move compounds into the cell)
– Enzymes (metabolism)
– Carriers (transport fats and oxygen in blood)
– Change size: movement (form muscles)
– Support and structure (form cartilage, bone, hair, fingernails)
– Immune defenses (antibodies, signals)
– & more...
Nucleotides build nucleic acids
 Two major classes – DNA and RNA
Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus
The nucleotide is composed of a N-containing base, a pentose sugar, and a
phosphate group
 Five nitrogen bases nucleotide structure
–adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U)
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Deoxyribonucleic Acid (DNA)
 Double-stranded helical molecule found in the nucleus of the cell
 Replicates itself before the cell divides, ensuring genetic continuity
 Provides instructions for protein synthesis
 Inherited from parents in chromosomes
Uses for nucleotides and nucleic acids:
 Nucleic acids
– DNA (information storage)
– RNA (information usage- genes to build proteins)
 Nucleotides
– Energy transfer (ATP)
– Build nucleic acids
ATP (adenosine triphosphate) is a type of molecule that provides all the energy to cells.
When food is broken down to glucose for energy, ATP is what is released, which is the
actual energy molecule. The more ATP that is produced, the more energy we have. When
we inhale oxygen, it is used in a process called respiration, which produces ATP for
energy. That is why we breathe. Just remember that ATP is an energy molecule.
This previous information will be useful in understanding proper nutrition, and genetic
defects. Now that you understand what these molecules are, in the cells lecture, we’ll talk
about what a typical cell in our body looks like. First, let’s talk about free radicals (cause
cancer) and ketones (complication of diabetes).
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Oxidation and Reduction
Oxidation is the loss of electrons or an increase in oxidation state by a
molecule, atom, or ion.
Reduction is the gain of electrons or a decrease in oxidation state by a molecule,
atom, or ion.
Free Radicals
Free radical reactions are redox reactions that occur as a part of homeostasis and
killing microorganisms, where an electron detaches from a molecule and then
reattaches almost instantaneously.
Free radicals are a part of redox molecules and can become harmful to the human
body if they do not reattach to the redox molecule or an antioxidant.
Unsatisfied free radicals can spur the mutation of cells they encounter and are thus
causes of cancer.
In general, the electron donor is any of a wide variety of flavoenzymes (anything that
requires FAD (flavin adenine dinucleotide) as a prosthetic group that functions in
electron transfers).
Once formed, these positively charged free radicals reduce molecular oxygen to
superoxide (O2-, from adding an electron).
The net reaction is the oxidation of the flavoenzyme and the reduction of molecular
oxygen to form superoxide.
Ketones
How do ketones form and how do they cause damage?
How do diabetics get ketones?
How do ketones cause coma in diabetics?
Ketogenic diet
The ketogenic diet is a high-fat, adequate-protein, low-carbohydrate diet that in
medicine is used primarily to treat difficult-to-control epilepsy in children.
The diet forces the body to burn fats rather than carbohydrates.
People who want to lose weight may go on a low-fat, low-carb diet, which will also
generate ketones.
Normally, the carbohydrates contained in food are converted into glucose, which is
then transported around the body and is particularly important in fuelling brain
function.
However, if there is very little carbohydrate in the diet, the liver converts fat into fatty
acids and ketone bodies.
The ketone bodies pass into the brain and replace glucose as an energy source.
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Ketone
“Ketone” comes from the word “acetone”. A ketone is an oxygen atom joined to a carbon
atom by a double bond, and the carbon is also bonded to two other carbon atoms.
Many ketones are of great importance in industry and in biology. Examples include
many sugars (ketoses) and the industrial solvent acetone.
Ketones are acidic, and if they build up in the blood, they will cause acidosis (low
blood pH).
Many sugars are ketones, known collectively as ketoses. The best known ketone is
fructose.
Ketosis
A metabolic state in which the body produces ketones to be used as fuel by some organs
so that glycogen can be reserved for organs that depend on it. This condition occurs
during times of fasting, starvation, or while on a low-carbohydrate weight-loss diet.
In medicine, acetone, acetoacetate, and beta-hydroxybutyrate are collectively called
ketone bodies. They are generated from the break-down of carbohydrates, fatty acids,
and amino acids. Ketone bodies are elevated in the blood (ketosis) and urine after fasting
(including a night of sleep or starvation). They can also be elevated if a diabetic takes too
little insulin, by the following process:
The pancreas secretes insulin when there is food in the stomach. Insulin is a substance
that takes glucose from the blood and transports it into each cell of the body, where it can
be broken down into ATP. Any excess glucose is taken to the liver and stored. When no
food has been eaten, insulin is no longer secreted. When insulin levels are low, the
pancreas then releases a hormone called glucagon. That causes the liver to release its
stored glucose into the bloodstream to raise the blood sugar levels back to normal, to be
sure the brain has enough glucose.
However, if the person does not make insulin because they have diabetes, and if they eat
a meal and do not give themselves an insulin shot, the low levels of insulin will trigger
the pancreas to release glucagon to raise the sugar levels, even though the person already
has high sugar levels from the meal they just ate. Now they have REALLY high blood
glucose levels, but without the insulin, the glucose cannot be taken into the cells to be
used. So the body is actually starving, and they will have to switch to breaking down fat
instead, which produces the acidic ketone bodies that cause most of the symptoms and
complications of ketoacidosis.
Ketoacidosis
Ketoacidosis is a severe form of ketosis, most commonly seen in diabetics, in which so
much ketone is produced that acidosis occurs (low blood pH). Symptoms include
vomiting, dehydration, deep gasping breathing, confusion and occasionally coma and
death.
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Diabetic coma is a reversible form of coma found in people with diabetes mellitus. It is
a medical emergency.
There are three different types of diabetic coma :
1. Severe diabetic hypoglycemia
2. Diabetic ketoacidosis advanced enough to result in unconsciousness from a
combination of severe hyperglycemia, dehydration and shock.
3. Hyperosmolar nonketotic coma in which
extreme hyperglycemia and dehydration alone are sufficient to cause
unconsciousness.
Ketone bodies
Any of several compounds that are intermediates in the metabolism of fatty acids;
principally acetoacetate and acetone. When fatty acids, sugars, or proteins are broken
down, ketone bodies form.
Ketone bodies
Ketone bodies are three different water-soluble, biochemicals that are produced by the
liver from fatty acids during periods of low food intake (fasting) and starvation for cells
of the body to use as energy instead of glucose. Two of the three (acetoacetate, and betahydroxybutyrate) are used as a source of energy in the heart and brain while the third
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(acetone) is a degradation breakdown product of acetoacetic acid. Ketone bodies are
picked up by cells and converted back into acetyl-CoA which then enters the citric acid
cycle and electron transport chain for energy.
Ketone bodies can be used for energy. In the brain, ketone bodies are a vital source of
energy during fasting or strenuous exercise. The liver breaks down protein to produce
glucose during starvation, because the liver cannot use ketone bodies for energy. Ketone
bodies are transported from the liver to other tissues, where acetoacetate and betahydroxybutyrate can be reconverted to acetyl-CoA to produce energy, via the citric acid
cycle.
Acetone in low concentrations is taken up by the liver and undergoes detoxification and
is turned into lactate. Acetone in high concentrations due to prolonged fasting or a low
carbohydrate diet is absorbed by cells other than those in the liver and enters a different
pathway and is turned into pyruvate. Ketone bodies are produced from acetyl-CoA
mainly in the mitochondria of hepatocytes (liver cells) when carbohydrates are so scarce
that energy must be obtained from breaking down fatty acids. Excess acetyl-CoA is
created, and it then makes ketone bodies.
Acetone is produced by the breakdown of acetoacetate, meaning this ketone body will
break down in five hours if it is not used for energy and be removed as waste, or
converted to Pyruvate. This "use it or lose it" factor may contribute to the weight loss
found in ketogenic (low carbohydrate) diets. Acetone cannot be converted back to acetylCoA, so it is excreted in the urine, or (as a consequence of its high vapor pressure)
exhaled. Acetone is responsible for the characteristic "Sweet & fruity" odor of the breath
of diabetics in ketoacidosis.
The heart prefers to use fatty acids for energy, but if the body has ketosis, it can use
ketone bodies for energy. The brain gets a portion of its energy from ketone bodies when
glucose is less available (e.g., during fasting, strenuous exercise, low carbohydrate diet).
In the event of low blood glucose, most other tissues have additional energy sources
besides ketone bodies (such as fatty acids), but the brain has an obligatory requirement
for some glucose. After the diet has been changed to lower blood glucose for 3 days, the
brain gets 25% of its energy from ketone bodies. After about 4 days, this goes up to 70%.
Ingestion of 3000 mg of omega-3 fatty acids per day produces enough ketones to
decrease oxidative damage in the body, and it also supplies the brain with enough ketones
to reduce cognitive deterioration in old age. You should get your omega-3 fatty acids
from flaxseed oil instead of fish oil to avoid hypervitiminosis (vitamin A, D, and E
toxicity).
Ketosis and ketoacidosis
In normal individuals, there is a constant production of ketone bodies by the liver, and
they are used by other organs. The concentration of ketone bodies in blood is maintained
around 1 mg/dl. Their excretion in urine is very low and undetectable by routine urine
tests (You would need the Rothera's test to detect ketones in the urine).
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