Download The Chemical Basis for Life Chapter 2

STRENGTH
“Do not pray for easy lives. Pray to be stronger
men! Do not pray for tasks equal to your powers.
Pray for power equal to your tasks."
-Phillips Brooks
CHAPTER 2
The Chemical basis of Life
Matter
• Anything that occupies space and has
mass.
• Can exist as:
• ____________
• ____________
• ____________
• composed of elements
• What are examples of each type
of matter?
What is an element?
• Element- substances that can not be
separated into smaller substances by
natural means.
• 92 of the 112 occur in nature
• 2 additional elements are
hypothetical (114, 116)
• And 2 more are not known to exist
(113, 115)
• Are referred to by a chemical symbol
and are organized in the Periodic
Table of Elements.
Elements in Animal Body
• Major Elements- make up 96% of the body
• ___________(O)
• ___________(C)
• ___________ (H)
• ___________ (N)
Minor Elements
• _______________ (Ca)
• _______________(P)
• _______________ (K)
• _______________(S)
• _______________(Na)
• _______________ (Cl)
• ________________ (Mg)
Trace Elements
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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 3 subatomic particles:
• ___________
• ___________
• ___________
Protons, Neutrons, & Electrons
•
•
Protons and Neutrons are
found in the
_____________________.
Each proton and neutron has
an atomic mass of ~1.
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•
•
Together protons and neutrons
determine the
__________________of the
atom.
Protons have a
_______________ charge.
Neutrons have
______________charge and
are considered neutral.
Electrons have a
_____________ charge.
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.
• Electrons have a ________________
charge.
• Orbit around nucleus
Electron Shells and
how they work
• “Pathways” around the nucleus where
electrons orbit
• Only a certain number of electrons can
be on each path at one time
• If the outermost shell is not full, then an
atom will be more active in an attempt
to fill its outermost shell.
• Helium and Neon have full electron
shells so are considered chemically
___________.
How the Shells work
• First shell can contain ________ electrons.
• Second shell on can contain _________
electrons.
Atoms continued
• The atomic number of an atom tells us
how many ____________ and
____________ it has.
• If an atom loses or gains an electron in an
attempt to fill its outermost electron shell
then it becomes positively or negatively
charged, thereby becoming an
_______________.
• If an atom has a different number of
neutrons, they are called
______________________ of the element
Atomic Number
Isotopes
Ions
e-
Na atom
Na+ ion
11electrons, 11protons
10electrons,
11protons
Molecules and Compounds
• ___________________- when atoms are
joined together by chemical bonds. These
are the smallest particle of a substance
that retains the properties of the
substance.
• _____________________when two or
more atoms of the same element are
joined together.
• _______________- how atoms are
attached to one another.
• ________________ A substance made up
of two or more elements.
Chemical Bonds
• Means that the atoms are sharing or
transferring electrons between them.
• By sharing or giving away electron,
each atom can be sure that its
outermost shell is full.
• Remember that atoms are constantly
trying to become more stable.
• Types of chemical bonds:
• _________________
• _________________
• _________________
Covalent Bonds
• Bonds formed when atoms share electrons.
• Classified depending on how many electrons are
being shared.
• single covalent bond — ______ electron is shared
• double covalent bond — _____ electrons are shared
• triple covalent bond — ______ 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 __________atom
than __________ atoms
• Created ‘poles’
• Gives molecule a slight _________ charge on H side of molecule and
slight _________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.
• Transfer causes a ______ charge on
the atom that gave up the electron and
a ____________ charge on the atom
that receives the electron.
• Since opposites attract, the two atoms
stick together through electrostatic
attraction.
Electron transferred
Attraction between
opposite charges
Types of Ions
• ______________- Ions with a net positive
charge.
• _______________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
• Bond between hydrogen atoms already
covalently bonded in a molecule to oppositely
charged particles.
• Found between water molecules and 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. Example:
• 2. Decomposition Reaction- single complex chemical is
broken down into multiple, simpler, chemicals. Example:
• 3. Exchange Reaction- certain atoms are exchanged
between molecules. Combination of synthesis and
decomposition reaction. Example:
Chemical Reactions Continued
• _____________ reactions require energy.
• ______________ reactions expend or
release energy.
• _______________have no net energy
requirements. Energy released from
decomposition portion, helps with
synthesis portion.
Chemical Reactions Continued
• Factors that influence reaction rates
• ________________________
• ________________________
• __________________-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
Why is water so Important?
• Water is the universal _______________
• ______________- chemicals added to water
• _______________- resulting chemical and water
mixture
• ________________ (water loving)- chemicals that
dissolve well or mix with water.
• _________________(water hating)- chemicals or
molecules that do not mix well with water.
• Water is an ideal ______________________
• Blanketing power allows molecules in water to
move around and be cushioned from one another.
• Blood
• Urine
• Water has a _______________and a high
_______________________________
• Easily able to absorb heat.
• Won’t evaporate easily.
• Water is used for ________________.
Salts
• Mineral compounds that have ionic bonds
• In ionic form are called electrolytessubstances that have ability to transmit an
electrical charge.
Acids and Bases
• ___________- substances that when
added to water freely release hydrogen
ions.
• Called H donors or proton donors
• ___________- alkaline in nature release a
hydroxyl ion (OH-) when added to water.
• 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 _______________.
Organic Molecules
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Molecules that contain carbon.
• Why carbon?-4 outer electrons in outer shell, trying
to share this to complete outer shell.
Divided into 4 groups:
• _____________________
• Glycogen
• Ribose
• ____________________
• Triglycerides
• Phospholipids
• Steroids
• Prostaglandins
• _____________________
• Globular
• Fibrous
• _____________________
• DNA
• RNA
• Adenosine triphosphate (ATP)
Carbohydrates
• Used for energy, storage of energy, and
cellular structures.
• Simple Sugars-________________.
• Glucose and Fructose
• ________________- when two
monosaccharides are joined together in
synthesis reaction.
• _________________- combinations of many
monosaccharides.
• Glycogen and cellulose
Some terminology
• _________________- when a
macromolecule is formed out of a
carbohydrate attached to a protein.
• __________________- process of building
molecules needed for cellular functioning.
• _____________________- Decomposition
of nutrients.
Lipids
• Used for energy and stored in fat.
• 4 classes of Lipids:
• _________________
• _________________
• _________________
• _________________
Lipids continued..
• Neutral Fats
• Also called triglycerides or fats.
• Contains three fatty acids and a glycerol
molecule.
• _________________________- all bonds in the
hydrocarbon chain are single bonds.
• _________________________- when there are
some double bonds between the carbon and
hydrogen atoms.
• __________________________macromolecule composed of proteins and lipids
• __________________________- when
triglycerides are decomposed.
• Phospholipids
• Have a glycerol backbone
• Have a lipid bilayer when placed in
water.
• ________________ heads are facing
water, while _______________ 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:
• _______________- in inflammation
• _______________- platelet function
• _______________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.
• Composed of ___________________
Amino Acids
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•
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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:
• ____________________- 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.
• Aka Fibrous proteins.
• Important in structural framework and
physical movement.
• Examples include:
• _______________
• _______________
• _______________
Functional Proteins
• Aka 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 ___________ or speed up
chemical reactions.
• Will end in –ase
• ______________ – the substance that the
enzyme acts upon.
Nucleic Acids
• Largest molecule of body
• 2 classes of Nucleic Acids
• _______________________________
• Exists mainly in the nucleus but also
mitochondria.
• Contains all instructions needed by cell to
build proteins.
• Coded in segments called __________
• _______________________________
• 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 _____________.
• Sugar in RNA is _____________.
• Nucleotides are named for their
nitrogen base.
• A,C,T,G,U
Structure of a nucleotide
Nucleotides
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A___________-both DNA and RNA
G___________-both DNA and RNA
C___________-both DNA and RNA
T___________-Only in DNA
U___________- Only in RNA
Nucleic Acids
• Information needed to produce proteins is
based on order of the nucleotides in DNA
and RNA.
• C-G-T makes amino acid alanine.
• ___________________-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 __________
• __________ and Cytosine
• Once bound, these two strands twist
around one another to form a
______________.
• Order of nucleotides is what makes unique
genetic code of each individual.
Structure of DNA
RNA
• Consists of only one strand of nucleotides.
• Does not have thymine, but instead has uracil.
• Pairings are:
• Guanine and Cytosine
• Adenine and __________
• Exists in three forms:
• tRNA- _________RNA
• Copies information in the DNA molecule
• mRNA- __________RNA
• Carries information out of the nucleus
• rRNA-___________ RNA
• Creates the proteins needed by the body
ATP
• ____________________- energy of the cells.
• Cells need ATP to fuel or carry out any work.
• _____________________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.