Chapter 2
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Transcript of Chapter 2
Chapter 2
The Chemical Level of
Organization
Introduction
Since chemicals compose your body (and all body activities are chemical in nature), it is important to become familiar with the language and fundamental concepts of chemistry.
How Matter is Organized All forms of matter are composed of chemical elements
which are substances that cannot be split into simpler
substances by ordinary chemical means.
– Elements are given letter abbreviations called chemical
symbols.
– Trace elements are
elements in our
bodies, present in
tiny amounts .
Structure of Atoms Units of matter of all chemical elements are called
atoms. An element is a quantity of matter composed
of atoms of the same type. Atoms contain:
Nucleus: protons
(p+) & neutrons
(no)
Electrons (e-)
surround the
nucleus as a
cloud
Electrons are very small and light (mass about 1/2000th that of proton or neutron), often represented as a “planet” orbiting the “sun” (atomic nucleus). In reality, they are found in a “cloud” of probability. This concept, however, made even Einstein’s head hurt – we can use the planets-orbiting-the-sun model for this course!
Structure of Atoms
Mass is measured as a dalton (atomic mass unit).
– Masses of subatomic particles
Neutron - mass of 1.008 daltons
Proton - mass of
1.007 daltons
Electron has mass of
0.0005 dalton
Structure of Atoms
– Atomic number is the number of protons in an
atom.
– Mass number is the sum of protons and neutrons
in an atom and indicates how much the atoms
“weighs”—this is always a whole number.
– Atomic mass (atomic weight) is the average mass
of all naturally occurring isotopes—since this is an
average, it is not exactly a whole number.
Structure of Atoms
Structure of Atoms
Ions, Molecules, & Compounds Ions are atoms that have given up or gained
an electron in their outer electron shell (also called the valence shell).– Written with its chemical symbol and (+)
or (–)
Ions, Molecules, & Compounds Molecules are formed when atoms share electrons.
– Written as a molecular formula showing the number of atoms of each element (H2O)
– The oxygen gas in the atmosphere we breath is really not oxygen the atom, but a pair of oxygen atoms linked together into an oxygen molecule (O2) .
Compound
A free radical is an electrically charged atom or group of
atoms with an unpaired electron in its outermost shell.
Antioxidants are substances that inactivate oxygen-
derived free radicals.
Ions, Molecules, & Compounds
Chemical Bonds The atoms of a molecule are held together by
forces of attraction called chemical bonds.
Valence shell.
Ionic Bond
Formation
Chemical Bonds
Covalent bonds are formed by the atoms of molecules sharing one, two, or three pairs of their valence electrons.– Covalent bonds are the strongest chemical bonds.– Single, double, or triple covalent bonds are
formed by sharing one, two, or three pairs of electrons, respectively.
Chemical Bonds
Hydrogen bonds are weak interactions (approximately 5% as
strong as covalent bonds) between hydrogen and adjacent
electronegative atoms like oxygen or sulfur.
Chemical Bonds
Hydrogen bonds are useful in establishing links between molecules or between distant parts of a very large molecule. Large 3-D molecules (like proteins) are often held together by a great many hydrogen bonds.In water, hydrogen bonding provides considerable cohesion which creates a very high surface tension (as this bug demonstrates).
Chemical Bonds
Chemical ReactionsChemical reactions occur when electrons in
the valence shell are shared or transferred. New bonds form and/or old bonds are broken.
Metabolism is the “sum of all the chemical reactions in the body”.
Law of conservation of energy:– The total mass of reactants equals the
total mass of the products .
Energy (the capacity to do work) is transferred in a chemical reaction.
Kinetic energy is the energy of matter in motion.
Potential energy is energy stored by matter - due to an object’s position in space, or stored in chemical bonds.
Chemical Reactions
Exergonic reactionsEndergonic reactions
Chemical Reactions
Activation Energy is the energy required to break chemical bonds in the reactant molecules so a reaction can start.
Chemical Reactions
Factors that cause a collision
- temperature
-concentration of the reactants,
-presence or absence of a catalyst.
Catalysts are chemical compounds that
speed up chemical reactions by lowering
the activation energy needed for a reaction
to occur.
Chemical Reactions
In a chemical reaction, a catalyst helps to properly orient the colliding particles
Chemical Reactions
Types of chemical reactions can be broadly classified as:
– Synthesis reactions – Anabolism
A + B ➙ AB
– Decomposition reactions – Catabolism
AB ➙ A + B
– Exchange reactions
AB + CD ➙ AD + CB– Reversible reactions
AC ↔ A + C
Chemical Reactions
Inorganic & Organic CompoundsInorganic compounds are structurally simple molecules that usually lack carbon - like the salt potassium chloride (KCl) depicted here:
Organic compounds always contain carbon and are usually large, complex molecules.
– Usually contain hydrogen
– Always have covalent bonds
Water is the most important and abundant inorganic compound in all living systems.
Water’s most important property is polarity, the uneven sharing of valence electrons that enables reactants to collide to form products.
Inorganic Compounds
Inorganic CompoundsSodium and Chloride ions dissolve in the polar
water molecules.
Water as a solvent:
– In a solution, the solvent dissolves the solute.
– Substances which contain polar covalent bonds and
dissolve in water are hydrophilic, while substances
which contain non-polar covalent bonds are
hydrophobic.
– Water’s role as a solvent makes it essential for
health and survival.
Inorganic Compounds
Water has a high heat capacity, meaning it can
absorb or release a relatively large amount of heat
with only a modest change in its own temperature.
This property is due to the large number of
hydrogen ions in water.
Heat of vaporization (amount of heat needed to
change from a liquid to a gas) is also high.
– Evaporation of water from the skin removes large
amounts of heat.
Inorganic Compounds
A mixture is a combination of elements or compounds
that are physically blended together but are not bound
by chemical bonds.
In a solution, a substance called the solvent dissolves
another substance called the solute. Usually there is
more solvent than solute in a solution.
– In our bodies, the most common solvent is water: We
are 65-80% water (depending on age - babies are very
“wet”… as anyone who has had one can attest.)
Three Common Mixtures
A colloid differs from a solution mainly on the basis of the size of its particles, with the particles in the colloid being large enough to scatter light (milk).
In a suspension, the suspended material may mix with the liquid or suspending medium for some time, but it will eventually settle out (blood is a suspension.)
Three Common Mixtures
The convenience is that one mole of hydrogen atoms weighs 1.01 grams, the same in grams as the atomic mass of hydrogen in Daltons.– 1 mole of oxygen atoms = 15.999 grams– 1 mole of sodium atoms = 22.989 grams– 1 mole of any atom or molecule is found in the
atomic mass of that element, or the molecularmass of that compound.
Methods of Measurement
The concentration of a molecule is a way of
stating the amount of that molecule in solution.
Percent gives the relative mass of a solute found in
100 ml of solution (usually water).
A mole is just a convenient way of counting large numbers of small things (like atoms or molecules).– 1 mole is 6.02 x 1023 of something just like 1 dozen
is 12 of something.
Methods of Measurement The concentration of a molecule is a way of
stating the amount of that molecule in solution.
Percent gives the relative mass of a solute found in
100 ml of solution (usually water).
A mole is just a convenient way of counting large numbers of small things (like atoms or molecules).– 1 mole is 6.02 x 1023 of something just like 1 dozen
is 12 of something.
Methods of Measurement
Acid – Dissociates into one more hydrogen ions
Base – Dissociates into one or more hydroxide ions
Salt – Dissociates into cations and anions
Inorganic acids and bases
pH = –log[H+] (concentration of H+
in moles/l)
It is a scale that runs from 0 to 14
Acids, Bases and Buffers
pH < 7 is acidic
([H+] > [OH-]);
pH > 7 is alkaline
([H+] < [OH-])
A salt (like KCl) is
neutral
The pH values of different parts of the body are maintained fairly constant by buffer systems, which usually consist of a weak acid and a weak base.– Buffers convert strong acids and strong
bases into weak acids and weak bases. They do this by “hiding” excess H+ ions or excess OH– ions as other molecules (like HCO3
– ) .– The major buffer system in the body is
carbonic acid-bicarbonate buffer system.
Acids, Bases and Buffers
Functional groups are certain molecular configurations which are easy to recognize.
They are found attached to the carbon skeleton and impart certain properties to the organic molecule.
Some of the more common functional groups are:
– Esters, amino, carboxyl, phosphate groups – Others are found on the following chart
(next slide)
Organic Compounds
Organic Compounds
Organic Compounds
Organic Compounds
Very large molecules are called macromolecules (or “polymers” if all the monomer subunits are similar).
Isomers have the same molecular formulas but different structures (glucose & galactoseare both C6H12O6).
Organic Compounds
Carbohydrates provide most of the energy
Some carbohydrates are converted to other substances which are used to build structures and to generate ATP.
Other carbohydrates function as food reserves.
Carbohydrates are divided into three major groups based on their size: monosaccharides, disaccharides, and polysaccharides .
Organic Compounds
Monosaccharides (Carbohydrates)
are the simplest sugars:– 5 carbon sugars are used in
nucleic acids.
– 6 carbon sugars are the most
easily recognizable in our diet.
Organic Compounds
Disaccharides are made by combining 2
monosaccharides by removing a water
molecule (dehydration synthesis):
sucrose = glucose + fructose
lactose = glucose + galactose
Organic Compounds
Polysaccharides are the largest carbohydrates and may contain hundreds of monosaccharides.
The principal polysaccharide in the human body is glycogen, which is stored in the liver or skeletal muscles.
Organic Compounds
Lipids are another major group of organic molecules.
– Like carbohydrates, they contain carbon, hydrogen, and
oxygen; unlike carbohydrates, they do not have a 2:1 ratio
of hydrogen to oxygen.
Organic Compounds
Triglycerides are the most plentiful lipids in the body and provide protection, insulation, and energy (both immediate and stored).– At room temperature, triglycerides may be
either solid (fats) or liquid (oils).– Triglyceride storage is virtually unlimited.– Excess dietary carbohydrates, proteins,
fats, and oils are deposited in adipose tissue as triglycerides.
Organic Compounds
Triglycerides provide more than twice as
much energy per gram as either
carbohydrates or proteins.
Organic Compounds
Phospholipids are important membrane components.
Both polar and nonpolar regions make them soluble in both water and fats (this is called amphipathic—they are both hydrophilic and lipophilic.)– They have a polar head formed from a
phosphate group (PO4-3) & a glycerol
molecule (forms H-bonds with water), and 2 nonpolar fatty acid tails that interact only with lipids.
Organic Compounds
Phospholipids have a polar head and 2 non-
polar tails:
Organic Compounds
Steroids are lipids molecules that have four rings of carbon atoms. They include: – Sex hormones– Bile salts– Some vitamins– Cholesterol, which serves as an important
component of cell membranes and as starting material for synthesizing other steroids
Organic Compounds
Steroids are based on the lipid cholesterol molecule.– They include the molecules used as sex hormones,
as well as other hormones used in coping with stress (cortisol).
Organic Compounds
Proteins are large molecules that contain
carbon, hydrogen, oxygen, and nitrogen.
This graphic is a model of an
enzyme protein.
Organic Compounds
Proteins are constructed from combinations of different amino acids.
The structures of 6 of the 20 human amino acids are depicted below:– All amino acids (a.a.)have the same basic structure– only the “R” group changes.
Proteins
Dipeptides are formed from 2 amino acids joined by a covalent bond called a peptide bond.– This process involves dehydration
synthesis.Polypeptide chains contain 10 to 2000
amino acids.
Proteins
There are 4 levels at which proteins are structurally organized :– Primary– Secondary– Tertiary– Quaternary
The resulting shape of the protein greatly influences its ability to recognize and bind to other molecules.
Proteins
The 4 levels of protein structural organization are depicted:
– Denaturation (loss of protein structure) by a hostile
environment causes loss of
its characteristic shape
and function.
– An egg white turning
solid white when exposed
to high temperatures is an
example of protein
denaturation.
Proteins
Enzymes are special proteins that catalyze (speed up) metabolic reaction in all living cells.
The substrate is the substance upon which an enzyme has its effect. In this regard, enzymes are highly specific.
Enzymes are subject to a variety of cellular controls.
Enzymes speed up chemical reactions by increasing frequency of collisions, lowering activation energy, and properly orienting colliding molecules.
Proteins
Nucleic acids are huge organic molecules composed of monomeric nucleotides (like the one shown below):– They contain carbon, hydrogen, oxygen, nitrogen,
and phosphorus, and form the principle molecules that contain our genetic code – DNA and RNA.
Organic Compounds
Nucleic acids are universal in living things.
These molecules carry genetic information
as deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA).
– By controlling the formation of
proteins, the genetic code
regulates most of the activities
that take place in our cells
throughout a lifetime.
Nucleic Acids
Nucleic AcidsDNA molecules remain inside the nucleus of
cells and are the “master” template of our genetic code.
RNA is a slightly different nucleic acid macromolecule that relays instructions from the nucleus to guide assembly of amino acids into proteins in the cytoplasm.
The basic units of nucleic acids are nucleotides, composed of a nitrogenous base, a pentose sugar, and a phosphate.
The nucleotides of DNA and RNA are joined to a “sugar-phosphate” backbone to make a long chain.
There are 2 sugar-phosphate strands of DNA, joined in the middle by hydrogen bonds from one nucleotide to another.
Nucleic Acids
RNA structure differs from DNA in that it is single
stranded (instead of double stranded), ribose
replaces the sugar deoxyribose, and uracil is the
nitrogenous base that replaces thymine.
There are 3 types of RNA within the cell,
each with a specific function:
– Messenger RNA
– Ribosomal RNA
– Transfer RNA
Nucleic Acids
ATP is often called the “molecular unit of currency”
of intracellular energy transfer.
Synthesis of ATP is catalyzed by the ATP synthase
enzyme which adds the terminal high energy
phosphate bond (often depicted as ~P as opposed to
a regular –P bond) to ADP.
– Energy from 1 glucose molecule is used during
both anaerobic and aerobic respiration to create 36
to 38 molecules of ATP.
Nucleic Acids
Nucleic Acids
When needed, the high energy phosphate is hydrolyzed by the enzyme ATPase to release the stored energy, leaving ADP (adenosine diphosphate).
A human will use up his/her body weight of ATP over the course of the day. This means that each ATP molecule is recycled 1500 times during a single day.
Nucleic Acids