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The Chemical Basis for Life
Chapter 2
Matter
• Anything that occupies space and has
mass.
• Can exist as:
• Gas
• Liquid
• Solid
• Is composed of elements
• What are examples of each type
of matter?
• Element- any of 116 known substances
that can not be separated into smaller
substances.
• 92 occur in nature
• 2 are hypothetical
• And 2 are not known to exist
• Are referred to by a chemical symbol
and are organized in the Periodic Table
of Elements.
• Nitrogen (N), Oxygen (O), Hydrogen
(H), and Carbon (C) make up 96% of
the matter found in all living organisms
Elements in Animal Body
• Major Elements
• Oxygen (O)
• Necessary for cellular energy
• Carbon (C)
• Primary component of organic molecules
• Hydrogen (H)
• Component of water and organic molecules,
necessary for energy transfer and
respiration
• Nitrogen (N)
• Component of all proteins and nucleic acid
•
Minor Elements
• Calcium (Ca)
• Bones, teeth, muscle contraction, nerve impulse
transmission
• Phosphorus (P)
• Energy transfer
• Potassium (K)
• Important in nerve function. Principle positive ion within
cells
• Sulfur (S)
• Component for most proteins
• Sodium (Na)
• Ion in extracellular fluid, important in nerve function.
• Chlorine (Cl)
• Most abundant neg ion in extracellular fluid
• Magnesium (Mg)
• Component of energy-transferring enzymes
•
Trace Elements
• Silicone (Si)
• Aluminum (Al)
• Iron (Fe)
• Manganese (Mn)
• Fluorine (F)
• Vanadium (V)
• Chromium (Cr)
• Copper (Cu)
• Boron (B)
• Cobalt (Co)
• Zinc (Zn)
• Selenium (Se)
• Molybdenum (Mo)
• Tin (Sn)
• Iodine (I)
Atoms
• The smallest unit of an element that
retains the unique properties of that
element.
• Composed of:
• Protons
• Neutrons
• Electrons
More about atoms-Protons and
Neutrons
• Protons and Neutrons are found in the
nucleus.
• Each proton and neutron has an atomic
mass of 1.
• Together protons and neutrons determine
the atomic weight of the atom.
• Protons have positive charge.
• Neutrons have no electrical charge and
are considered neutral.
• Net charge of atoms are neutral because
have equal numbers of protons and
electrons.
Electrons
• Tiny particles that remain in constant
motion around the nucleus.
• So tiny that their mass does not contribute
to the atomic weight of the atom.
• Have negative charge.
• Orbit around nucleus but not necessarily in
a planetary manner, more in an orbital
manner so that electrons exist in a cloud
and they can move closer to one side of
the atom or the other.
Atoms continued
• The number of protons gives an atom its
atomic number.
• If an atom loses or gains an electron, then
it becomes positively or negatively
charged, thereby becoming an ion.
• If an atom has a different number of
neutrons, then they are called isotopes of
the element
Atomic Number
Isotopes
Ions
e-
Na atom
Na+ ion
11 e, 11 p
10 e, 11 p
Rate of Decay
• The time rate of disintegration of
radioactive material, generally
accompanied by emission of particles or
gamma radiation.
Electron Shell
• Area around the nucleus where the
electrons are most likely to be.
• Electron’s energy level determines which
electron shell it will inhabit.
• Lower energy electrons will be closer to
nucleus in lower shells.
• If shells are not full, then atoms will be
more active.
• Helium and Neon have full electron shells
so are chemically inert.
How the Shells work.
• First shell can contain 2 electrons.
• Second shell on can contain 8 electrons.
Molecules and Compounds
• Molecules- when atoms are joined
together by chemical bonds. Are the
smallest particle of a substance that
retains the properties of the substance.
• Molecule of the element- when two or
more atoms of the same element are
joined together.
• Bonds- how atoms are attached to one
another.
• Compounds- A substance made up of two
or more elements.
Chemical Bonds
• Means that the atoms are sharing or
transferring electrons between them.
• Trying to fill their shells or give up extra
electrons to another atom.
• Remember that atoms are constantly
trying to become more stable.
• Types of chemical bonds:
• Covalent
• Ionic
• Hydrogen
Covalent Bonds
• Bonds formed when atoms share electrons.
• Electrons spend part of time in outer electron shell
of each atom.
• Classified depending on how many electrons are
being shared.
• single covalent bond — one electron is shared
• double covalent bond — two electrons are shared
• triple covalent bond — three electrons are shared
• May be shared equally (nonpolar) or unequally
(polar).
Polar Water Molecule
• Shared electrons in a covalently bonded molecule may spend more time
near one atom than the other
• Shared electrons in water molecule spend more time near O atom than H
atoms
• Created ‘poles’
• Gives molecule a slight positive charge on H side of molecule and
slight negative charge on O side of molecule
http://www.youtube.com/watch?v=qmgE0w6E6ZI
Ionic Bonds
• Formed when electrons are transferred
from one atom to another.
• Formed most often between two different
types of atoms.
• Usually between with fewer than 2
electrons in outer shell and those that
are nearly full.
• Transfer causes a positive charge on
one atom and a negative charge on the
other. Keeps attraction to one another
called electrostatic attraction.
Electron transferred
Attraction between
opposite charges
Types of Ions
• Cations- Ions with a net positive charge.
• Anions- Ions with a net negative charge.
• Ions are important in contraction of muscle
fibers, transmission of nerve impulses, and
maintenance of water balance.
Hydrogen Bonds
• A specific type of a weak ionic bond.
• Weaker than ionic or covalent bonds.
• Bond between hydrogen atoms already
covalently bonded in a molecule to
oppositely charged particles.
• Since Hydrogen wants to “donate”
electron, will have outer electron going
toward other nucleus. This will make
Hydrogen have an overall positive charge.
• Positive charge will cause electrostatic
attraction to a negative molecule.
• Found in water or DNA to stabilize shape.
Chemical Reactions
• The formation and breaking of chemical
bonds.
• Require energy input or release of energy.
• Chemical Equation- reaction is described
in written form.
• X+Y
→
Z
• (reactants)
(products)
• Arrow indicates direction of the reaction
Types of Chemical Reactions
• 1. Synthesis Reaction- new and more complex
molecule is made from simpler chemicals.
• X+Y→XY
• O + O = O2
• 2. Decomposition Reaction- single complex
chemical is broken down into multiple, simpler,
chemicals.
• XY→X+Y
• 2H20→2H2 + O2
• 3. Exchange Reaction- certain atoms are
exchanged between molecules. Combination of
synthesis and decomposition reaction.
• WX + YZ → WY + XZ
• NaHCO3 + HCl → NaCl + H20 + C02
Chemical Reactions Continued
• Synthesis reactions require energy.
• Decomposition reactions expend or
release energy.
• Exchange reactions have no net energy
requirements. Energy released from
decomposition portion, helps with
synthesis portion.
Chemical Reactions Continued
• Factors that influence reaction rates
• Concentration of reactants
• Temperature of environment
• Activation energy- the energy required
for the reaction to happen.
• Some reactions require presence of a
catalyst or enzyme
• Reaction speed is increased when
catalyst is present
• Protein (enzyme)
Chemical Components of Living
Organisms: Organic and Inorganic
Compounds
• Inorganic compounds- do not contain
hydrocarbon groups (H and C bonded
together) and often have ionic bonding.
• Water
• Salts
• Acids and Bases
• Organic compounds- contain hydrocarbon
groups and are usually covalently bonded
Water
•
•
•
•
Water is the universal solvent
• Solutes- chemicals added to water
• Solution- resulting chemical and water mixture
• Hydrophilic (water loving)- chemicals that dissolve
well or mix with water.
• Hydrophobic (water hating)- chemicals or molecules
that do not mix well with water.
Water is an ideal transport medium
• Blanketing power allows molecules in water to move
around and be cushioned from one another.
• Blood
• Urine
Water has a high heat capacity and a high heat of
vaporization
• Easily able to absorb heat.
• Won’t evaporate easily.
Water is used for lubrication.
Salts
• Mineral compounds that have ionic bonds
• Principal form of minerals that enter and
are stored in the body.
• In ionic form are called electrolytessubstances that have ability to transmit an
electrical charge.
Acids and Bases
• Acids- ionically bonded substances that
when added to water freely release
hydrogen ions.
• Called H donors or proton donors
• Bases- alkaline in nature release a
hydroxyl ion (OH-).
• Called proton acceptors
• Acids and Bases are also electrolytes as
they can transmit electricity when ionized
in water.
The pH Scale
• Ranges from 1-14.
• Lower numbers are the most acidic, higher
numbers are more alkaline.
Buffers
• A substance that minimizes the change of
the acidity of a solution when an acid or
base is added to the solution.
• By not allowing excessive hydrogen or
hydroxyl ions to accumulate, buffers help
cell maintain a neutral pH.
Organic Molecules
•
•
Molecules that contain carbon.
• Why carbon?-4 outer electrons in outer shell, trying to share this to
complete outer shell.
Divided into 4 groups:
• Carbohydrates
• Glycogen
• Ribose
• Lipids
• Triglycerides
• Phospholipids
• Steroids
• Prostaglandins
• Proteins
• Globular
• Fibrous
• Nucleic Acids
• DNA
• RNA
• Adenosine triphosphate (ATP)
Carbohydrates
• Used for energy, storage of energy, and
cellular structures.
• Simple Sugars-monosaccharides.
• Glucose and Fructose
• Disaccharide- when two monosaccharides
are joined together in synthesis reaction.
• Polysaccharides- combinations of many
monosaccharides.
• Glycogen and cellulose
Some terminology
• Glycoprotein- when a macromolecule is
formed out of a carbohydrate attached to a
protein.
• Anabolism- process of building molecules
needed for cellular functioning.
• Catabolism- Decomposition of nutrients.
Lipids
• Used for energy and stored in fat.
• 4 classes of Lipids:
• 1. Neutral fats
• 2. Phospholipids
• 3. Steroids
• 4. Eicosanoids
Lipids continued..
• Neutral Fats
• Also called triglycerides or fats.
• Contains three fatty acids and a glycerol
molecule.
• Saturated fatty acids- all bonds in the
hydrocarbon chain are single bonds.
• Unsaturated fatty acids- when there are some
double bonds between the carbon and
hydrogen atoms.
• Lipoproteins- macromolecule composed of
proteins and lipids
• Hydrolysis- when triglycerides are decomposed.
• Phospholipids
• Have a glycerol backbone
• Have a lipid bilayer when placed in
water.
• Hydrophilic are facing water, while
hydrophobic tails line up with one
another.
• Steroids
• Take form of four interlocking
hydrocarbon rings.
• Are hydrophobic.
• Examples include:
• Cholesterol
• Cortisol
• Eicosanoids
• Lipids formed from a 20 carbon fatty
acid and ring structure. (hairpin
structure)
• Include:
• Prostaglandins- in inflammation
• Thrombaxone- platelet function
• Leukotrienes- bronchoconstriction
and increased mucus production.
Proteins
• Most abundant organic molecules in the
body.
• Have widest variety of functions.
• Catalyze- speed up reactions occurring in
the body.
• Transport ions and other molecules into
and out of the cell and around the body.
• Made chiefly of carbon, oxygen, hydrogen,
and nitrogen.
• Composed of amino acids
Amino Acids
•
•
•
20 different amino acids used by the body.
Central carbon is attached to hydrogen atom, an amino group (NH2), a
carboxyl group (COOH), and a side chain.
Include:
Alanine
Arginine
Asparagine
Aspartic acid
Cysteine
Glutamic acid
Glutamine
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
Structure of Proteins
• Shape of protein directly determines its function.
• Antibodies- fit together like puzzle to foreign
invaders.
• Structure is described in four layers:
• Primary Structure- sequence and number of
amino acids that link together to form the
peptide chain.
• Secondary Structure- the natural bend of parts
of the peptide chain as it is formed in three
dimensions.
• Tertiary Structure- overall shape of a single
protein molecule.
• Quaternary Structure- when two or more protein
chains join to form a complex macromolecule.
• http://www.youtube.com/watch?v=Oz2x_y
xPXww&feature=related
Structural Proteins
• Stable, rigid, water-insoluble proteins that
are used for adding strength to tissues or
cells.
• May also be called Fibrous proteins.
• Important in structural framework and
physical movement.
• Examples include:
• Collagen
• Keratin
• Actin and Myosin
Functional Proteins
• Generally are water-soluble and have a flexible,
three-dimensional shape, which can change under
different circumstances
• May also be called Globular proteins.
• Function in chemical reactions, transport of
molecules, regulation of metabolism, and immune
system.
• Include:
• Hormones
• Antibodies
• Protein-based hormones
• Enzymes
Enzymes
• Proteins that catalyze or speed up
chemical reactions.
• Will end in –ase
• Are essential in the body for catalyzing
(speeding up) chemical reactions without
being destroyed themselves during the
process.
• Substrates – the substance that the
enzyme acts upon.
Nucleic Acids
• Largest molecule of body composed of Carbon,
Oxygen, Hydrogen, Nitrogen, and Phosphorus.
• 2 classes of Nucleic Acids
• DNA (deoxyribonucleic acid)
• Exists mainly in the nucleus but also
mitochondria.
• Contains all instructions needed by cell to
build proteins.
• Coded in segments called genes.
• RNA (ribonucleic acid)
• Transfers the instructions out of the nucleus
and into the cytoplasm and builds proteins.
• Exists as mRNA, tRNA, and rRNA.
Nucleotides
• The molecular building blocks of nucleic
acids.
• Are 5 different nucleotides, but all have the
same structure.
• Are all composed of a 5-Carbon
pentose sugar.
• Sugar in DNA is deoxyribose.
• Sugar in RNA is ribose.
• Nucleotides are named for their
nitrogen base.
Nucleotides
•
•
•
•
•
Adenine-both DNA and RNA
Guanine-both DNA and RNA
Cytosine-both DNA and RNA
Thymine-Only in DNA
Uracil- Only in RNA
Nucleic Acid Formation
• Occurs when sugar and phosphate groups
join in a long chain with nitrogenous base
open.
• Information needed to produce proteins is
based on order of the nucleotides.
• C-G-T makes amino acid alanine.
• Chromosomes-long chains of genes
combined with proteins.
DNA
• Consists of two parallel strands of
nucleotides adenine, guanine, cytosine
and thymine.
• Connected by hydrogen bonds between
specific pairings of nucleotides.
• Adenine and Thymine
• Guanine and Cytosine
• Once bound, these two strands twist
around one another to form a double helix.
• Order of nucleotides is what makes unique
genetic code of each individual.
RNA
• Consists of only one strand of nucleotides.
• Does not have thymine, but instead has uracil.
• Pairings are:
• Guanine and Cytosine
• Adenine and Uracil
• Exists in three forms:
• tRNA- Transfer RNA
• Copies information in the DNA molecule
• mRNA- Messenger RNA
• Carries information out of the nucleus
• rRNA-Ribosomal RNA
• Creates the proteins needed by the body
ATP
• Adenosine Triphosphate- energy of the cells.
• Cells need ATP to fuel or carry out any work.
• Cellular Respiration- when the cells use up the
nutrients
• ATP is a RNA nucleotide containing adenine with
two additional phosphate groups attached.
• When bonds (high energy bonds) between
phosphate groups are broken, energy is released.
• When phosphate group is lost, resulting molecule is
adenosine diphosphate (ADP).
Why is it so important?
• Since we know how these bonds work, we
can understand how certain things such as
drugs and chemical reactions in the body
occur.
• Will help us later on in digestion of food,
growth of the body, cellular signaling, and
transmission of nerve impulses.