PowerPoint Presentation - BIO 211: Chemical BasisofLife

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BIO 211
ANATOMY PHYSIOLOGY I
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CHAPTER 02
CHEMICAL BASIS OF LIFE
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
Dr. Lawrence G. Altman www.lawrencegaltman.com Som
e illustrations are courtesy of McGraw-Hill.
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I. Matter consists of chemical elements in pure
form and in combinations called
compounds Chemistry is fundamental to an
understanding of life, because livingorganisms
are made of matter. Matter Anything that takes
up space and has mass. Mass A measure of the
amount of matter an object contains.
There is a slight difference between mass and
weight. Mass is the measure of the amount
of matter an object contains it stays the
same regardless of changes in the object's
position. Weight is the measure of how
strongly an object is pulled by earth's
gravity, and it varies with distance from the
earth's center.
The important point is that the mass of a body
does not vary with its position, whereas weight
does. So, for all practical purposes - as long
as we are earthbound - weight can be used as a
measure of mass.
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II. Life requires about 25 chemical
elements Element A substance that cannot be
broken down into other substances by chemical
reactions. All matter made of
elements. 92 naturally occurring. Desig
nated by a symbol of one/two letters.
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Trace element Element required by an organism
in extremely minute quantities.
Though in small quantity, are indispensable
for life. For example B, Cr, Co,
Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V and Zn.
Ultratrace element Element required by an
organism in extremely minute quantities but
TOXIC at high levels. For example
Arsenic (Ar)
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II. Life requires about 25 chemical elements
(cont.) Elements can exist in combinations
called compounds. Compound A pure substance
composed of two or more DIFFERENT elements
combined in a fixed ratio. For
example NaCl (sodium chloride).
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III. Atomic structure determines the behavior of
an element Atom Smallest possible unit of
matter that retains (keeps) the physical and
chemical properties of its element. Atoms of
the same element share similar chemical
properties. Made up of subatomic particles.
A. Subatomic Particles The three most stable
subatomic particles are 1. Neutrons no
charge (neutral) 2. Protons
1 electrostatic charge 3. Electrons - 1
electrostatic charge
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Found together in a dense core called the atomic
nucleus. Nucleus is (due to
protons) 1.009 dalton 1.007 dalton Masses of
both are about the same (approx. 1 dalton)
NOTE The Dalton is used to express mass at the
atomic level.
If an atom is electrically neutral, the number
of protons EQUALS the number of electrons, which
yields an electrostatically balanced charge.
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• Atomic structure determines the behavior of an
  element (cont.)
• B. Atomic Number and Atomic Mass
• Atomic number Number of PROTONS in an atom
• of a particular element.

All atoms of an element have the same atomic
number. Written as a subscript to the
left of the element's symbol. Example
11Na In a neutral atom, protons
electrons.
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• Atomic structure determines the behavior of an
  element (cont.)
• B. Atomic Number and Atomic Mass
• Mass number Number of PROTONS NEUTRONS in
  an atom.
• Each has a mass of approx 1 dalton.

Written as a superscript to the left of an
elements symbol. Example 23 Na
Is the approximate mass of the whole atom, since
the mass of a proton and the mass of a neutron
are each equal to 1 dalton. dalton a
measurement of mass at the atomic level.

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• Atomic structure determines the behavior of an
  element (cont.)
• B. Atomic Number and Atomic Mass
• Mass number Can deduce the number of NEUTRONS
  by
• subtracting atomic number from atomic mass.
• Neutrons Mass number - Atomic number
• N (protons N) -
  (protons)

The number of Protons (the Atomic
number??) in an element is ALWAYS constant (the
same).. The number of Neutrons in an element
CAN vary.
Now, try a few problems.
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of electrons
of protons
of neutrons
of electrons
of protons
of neutrons
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• Atomic structure determines the behavior of an
  element (cont.)
• C. Isotopes
• Isotopes Atoms of an element that have the
• same atomic number but different mass
  number.

Have the same number of protons, but
different number of neutrons.
Atomic WEIGHT Weighted average of the mixture
Under natural conditions, elements occur
as mixtures of isotopes.
Different isotopes of the same element
react chemically in the same way.

Some isotopes are radioactive.
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• Atomic structure determines the behavior of an
  element (cont.)
• C. Isotopes
• Radioactive isotope Unstable isotope in which
  the nucleus spontaneously decays emitting
  sub- atomic particles and/or energy as
  radioactivity.
• Loss of nuclear particles may
  transform (change) one element to
  another !!

Has a fixed half - life
Half life Time for 50 of radioactive
atoms in a sample to decay.

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• Atomic structure determines the behavior of an
  element (cont.)
• C. Isotopes
• Biological applications of radioactive
  isotopes include
• 1. Dating geological strata (layers) and
  fossils.

2. Radioactive tracers Chemicals
labeled with radioactive isotopes are used
to trace the steps of a biochemical
reaction or to determine the location of a
particular substance within an organism.
Radioactive isotopes are useful as
biochemical tracers because they
chemically react like the stable isotopes
and are easily detected at low concentrations.
Isotopes of P, N and H were used to
determine DNA structure.
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• Atomic structure determines the behavior of an
  element (cont.)
• C. Isotopes
• Biological applications of radioactive
  isotopes include
• 2. Radioactive tracers (cont.)
• Used to diagnose disease (e.g. PET
  scanner).
• Because radioactivity can damage cell
  molecules, radioactive isotopes can also be
  hazardous.

3. Treatment of Cancer Example
radioactive cobalt.
D. Energy Levels Electrons Light negatively
- charged particles that orbit around a
nucleus. Are the only subatomic particles
which are directly involved in chemical
reactions. Cont. gtgtgt
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• Atomic structure determines the behavior of an
  element (cont.)
• D. Energy Levels (cont.)
• Energy Ability to do work.
• Potential Energy Energy that matter stores
  because of its position or location.

• E. Electron Configuration and Chemical
  Properties
• A electron configuration determines its
  chemical behavior.

Electron configuration Distribution of
electrons in an atom's electron shells.
Electrons must first occupy lower electron
shells before the higher shells can be
occupied. (A reflection of the natural tendenc
y for matter to move to the lowest possible state
of potential energy - the most stable state.)
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• Atomic structure determines the behavior of an
  element (cont.)
• E. Electron Configuration and Chemical
  Properties
• Chemical Properties of an atom depend upon
  the
• number of valence electrons.

Valence electrons Electrons in the outermost
energy shell (valence shell). Octet
rule Rule that a valence shell is complete
when it contains 8 electrons.
(except H He outer shell max. 2
e-).
smaller elements
An atom with a complete valence shell is
unreactive or inert. Noble elements (e.g.
helium, argon and neon) have filled outer
shells in their elemental state and are thus
inert. An atom with an incomplete valence
shell is chemically reactive (tends to form
chemical bonds until it has 8 electrons to
fill the valence shell).
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• Atoms Combine by Chemical Bonding to form
  Molecules.
• Atoms with incomplete valence shells tend to
  fill those shells by interacting with other
  atoms.
• These interactions of electrons among atoms
• may allow atoms to form chemical bonds.

Chemical Bonds Attractions that hold
molecules together. Molecule (2) atoms
held together via chemical bonds. Compound
molecule, also. BUT, contains (2) different
atoms.
A. Covalent Bonds (strongest among the top 3
types of bonds) Covalent bonds are chemical
bonds formed by sharing a pair of valence
electrons.
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• Atoms Combine by Chemical Bonding to form
  Molecules.
• A. Covalent Bonds (strongest among the top 3
  types of bonds)
• Structural formula Formula which represents
  the atoms and bonding within a molecule
  (e.g. H-H).
• The line represents a shared pair of
  electrons.
• Molecular formula Formula which indicates
  the
• number and type of atoms (e.g. H2)

• Single covalent bond Bond between atoms
  formed by sharing
• a single pair of valence electrons.

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(SINGLE)
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DOUBLE Bond actually- 2 double bonds.

Why??
O C O
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• Atoms Combine by Chemical Bonding to form
  Molecules.
• A. Covalent Bonds (strongest among the top 3
  types of bonds)
• Triple covalent bond Formed when atoms share
  three pairs of valence electrons (e.g.
  N2)
• Test it! ---- Atomic of N 7

• Valence Bonding capacity of an atom
  which is
• the number of covalent bonds that
  must be formed
• to complete the outer shell.

Valences of some common
elements Hydrogen 1 Oxygen
2 Nitrogen 3 Carbon
4 Phosphorous 3 Sulfur 2
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• Atoms Combine by Chemical Bonding to form
  Molecules.
• A. Covalent Bonds (strongest among the top 3
  types of bonds)
• Compound A pure substance composed of
  two or more (2) elements
• in a fixed ratio.

For example water
(H2O) methane (CH4)
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• Atoms Combine by Chemical Bonding to form
  Molecules.
• B. Ionic Bonds (second strongest among the top
  3 types of bonds)
• Ion Charged atom or molecule

• Anion An atom that has gained one or more
  electrons from another atom and has become
  negatively charged a negatively charged
  ion.
• Cation An atom that has lost one or more
  electrons and has become positively
  charged
• a positively charged ion.

Ionic bond Bond formed by the electrostatic
attraction after the complete transfer of
an electron from a donor atom to an
acceptor.

• The acceptor atom attracts the
  electrons because it is much more
  electronegative than the donor atom
• Are strong bonds in crystals, but are
  fragile bonds in water salt crystals
  will readily dissolve in water and
  dissociate into ions.

Ionic compounds are called salts. e.g. NaCl or
table salt
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NEXT SLIDE REVIEW
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• V. Hydrogen Bonding.
• Biologically, an important weak bond
• Can form between molecules or
• between different parts of a single large
  molecule.
• Example Integrity of DNA double - stranded
  molecule more

Hydrogen bond Bond formed by the charge
attraction when a hydrogen atom covalently
bonded to one electronegative
(electron-loving) atom is attracted to
another electronegative atom.
Weak attractive force that is about 20 times
easier to break than a covalent bond. Is
a charge attraction between oppositely charged
portions of polar molecules. Can occur
between a hydrogen that has a slight positive
charge when covalently bonded to an atom with
high electronegativity (usually 0 and N).
Example NH3 (ammonia) in H20.
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ELECTRONEGATIVE ATOMS (electron-loving)
HYDROGEN BOND (dotted line)
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• V. Hydrogen Bonding.
• Hydrogen Bonding orders water into a
• higher level of structural organization.

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VI. Chemical reactions change the composition of
matter Chemical reactions process of making
and breaking chemical bonds leading to
changes in the composition of
matter. Process where reactants
undergo changes into products.
The relative concentration of reactants and
products affects the reaction rate. (the higher
the concentration, the greater probability of a
reaction).
Matter is conserved, so all reactant
atoms are only rearranged to
form products.
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VI. Chemical reactions change the composition of
matter Chemical equilibrium Chemical
equilibrium Equilibrium established when the
rate of forward reaction equals
the rate of the reverse reaction.
Is a dynamic equilibrium with reactions
continuing in both directions. Relative
concentrations of reactants and products stay
the same.
NOTE Chemical equilibrium does NOT
mean that the concentrations of
reactants and products are equal.
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VII. Water is the solvent of life Solution
A liquid that is a homogenous
mixture of two or more
substances. Solvent Dissolving agent of a
solution. Solute Substance dissolved in
a solution. Aqueous solution Solution in
which water is the solvent.
VIII. Organisms are sensitive to changes in
pH A. Dissociation of Water
Molecules Occasionally, the hydrogen atom
that is shared in a hydrogen bond between two
water molecules, shifts from the oxygen atom
to which it is covalently bonded to the
unshared orbitals of the oxygen atom to
which it is hydrogen bonded.
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VIII. Organisms are sensitive to changes in
pH A. Dissociation of Water Molecules
(cont.) Only a hydrogen ion (proton with
a 1 charge) is actually transferred.
(H) Transferred proton (H) binds to an
unshared orbital of the second water
molecule creating a hydronium ion (H30)
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VIII. Organisms are sensitive to changes in pH
A. Dissociation of Water Molecules
(cont.) By convention, ionization of
H20 is expressed as a dissociation into H and
OH-. H20
H OH- Reaction is
reversible. At equilibrium, most of the
H20 is not ionized.
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VIII. Organisms are sensitive to changes in pH
B. Acids and Bases At
equilibrium in pure water at 25oC Number
of H ions number of OH- ions.
H OH- 1/10,000,000 M 10-7
M Note that brackets indicate molar
concentration. Very few water molecules are
actually dissociated (only 1 out of
554,000,000 molecules) !!!
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BASE
ACID
Substances that increase the relative H of a
solution.
Substances that reduce the relative H of a
solution.
Also removes OH- because it tends to combine
with H to form H2O.
May alternately increase OH- (see NaOH below)

A solution in which
H OH- is neutral H gt
OH- is acidic H lt OH- is basic
(alkaline)
LEO the lion says GER !!!
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VIII. Organisms are sensitive to changes in pH
C. The pH Scale
A solution in which
H OH- is neutral H gt
OH- is acidic H lt OH- is basic
(alkaline)
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VIII. Organisms are sensitive to changes in pH
C. The pH Scale
Discuss this on the board
pH -log H
Most biological fluids are within the
pH range of 6 to 8. There are some
exceptions such as stomach acid with pH
1.5.
Each pH unit represents a tenfold
difference (scale is logarithmic), so a
slight change in pH represents a large
change in actual H.
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VIII. Organisms are sensitive to changes in pH
D. Buffers By minimizing wide
fluctuations in pH, buffers help organisms
maintain the pH of body fluids within the
narrow range necessary for life (usually pH
6-8).
Buffer Substance that prevents large,
sudden changes in pH.
At this point in Bio. 225 no
need to completely know the equations of
the following example. However, the
concept of a buffer will be explained using
this example gtgtgtgtgtgt
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VIII. Organisms are sensitive to changes in pH
D. Buffers Are combinations of
H-donor and H-acceptor forms of weak acids or
bases. Work by accepting H ions from
solution when they are in excess, and by
donating H ions to the solution when they
have been depleted.
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IX. Biological Molecules NOTE Be able to
distinguish between organic (contains carbon
and hydrogen) and inorganic. I. Most
macromolecules (large) are polymers
Polymer Large molecule consisting of many
identical or similar subunits
connected together. Monomer Subunit or
building block molecule of a
polymer. Macromolecule (Macro large) Large
organic (carbon containing)
polymer. Formation of macromolecules from
smaller building block molecules represents
another level in the hierarchy of biological
organization.
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IX. Biological Molecules There are four classes
of macromolecules in living organisms 1.
Carbohydrates. 2. Lipids. 3. Proteins.
4. Nucleic acids. i.e., DNA, RNA and ATP
(which will be reviewed during metabolism).
Most polymerization reactions in living
organisms are condensation reactions (next
slide). Polymerization reactions Chemical
reactions that link two or more small
molecules to form larger molecules with
repeating structural units.
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IX. Biological Molecules Condensation
reactions (ANABOLISM) Polymerization
reactions during which monomers are covalently
LINKED, producing net removal of a water
molecule for each covalent linkage.
One monomer loses a hydroxyl (-OH), and the
other monomer loses a hydrogen (-H).
Process requires energy. Process
requires biological catalysts or enzymes.
SPLITTING polymers into monomers gtgtgtgtgt
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IX. Biological Molecules Hydrolysis (CATABOLIS
M) Hydro water lysis break) A
reaction process that BREAKS (SPLITS)
covalent bonds between monomers by the
addition of water molecules.
A hydrogen from the water bonds to one
monomer, and the hydroxyl (also from the
water) bonds to the adjacent monomer. For
example (and many more with illustrations to
follow) digestive enzymes catalyze hydrolytic
reactions which break apart large food
molecules into monomers that can be absorbed
into the bloodstream.
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X. Organisms use CARBOHYDRATES for Fuel and
Building Material. CARBOHYDRATES Organic
molecules made of sugars and their
polymers.
Monomers or building block molecules are
simple sugars called monosaccharides.

Polymers are formed
by condensation reactions. Are classified
based upon the number of simple sugars.
MONO (1 sugar), DI- (2 sugars) gtgtgtgtgt
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X. Organisms use CARBOHYDRATES for Fuel and
Building Material. MONOSACCHARIDES
(Mono single sacchar- sugar)
Simple sugar in which C, H and 0 occur in
the ratio of (CH20) Are major nutrients for
cells. Glucose is the most common.
Store energy in their chemical bonds which is
harvested by cellular respiration. Can be
incorporated as monomers into disaccharides and
polysaccharides.
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X. Organisms use CARBOHYDRATES for Fuel and
Building Material. DISACCHARIDES (DI
two sacchar- sugar) A double sugar
that consists of two monosaccharides joined by a
glycosidic linkage.
Glycosidic linkage Covalent bond formed by
a condensation reaction between two sugar
monomers. For example, maltose gtgtgtgtgtgtgtgtgtgtgt
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X. Organisms use CARBOHYDRATES for Fuel and
Building Material. DISACCHARIDES
A condensation !! (removing water to
combine---)
MALTOSE
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• Organisms use CARBOHYDRATES
• for Fuel and Building Material.
• DISACCHARIDES

Some IMPORTANT DISACCHARIDES
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X. Organisms use CARBOHYDRATES for Fuel and
Building Material. POLYSACCHARIDES
Macromolecules that are polymers of a few
hundred or thousand monosaccharides. Are
formed by linking monomers in enzyme-mediated
condensation (joining by removing water)
reactions.
STORAGE Polysaccharides Cells hydrolyze
storage polysaccharides into sugars as needed.
The most common storage polysaccharide in
animals is Glycogen Glucose polymer in
animals. (as starch in plants) Stored in
the muscle and liver of humans and other
vertebrates.
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XI. Lipids are mostly hydrophobic molecules with
diverse functions LIPIDS Diverse group of
organic compounds that are insoluble in water,
but will dissolve in nonpolar solvents (e.g.
ether, chloroform, benzene).
Important groups are Fats Pho
spholipids Steroids
A. Fats Macromolecules constructed
from 1. Glycerol, a three-carbon
alcohol. 2. Fatty acid (carboxylic
acid). Composed of a carboxyl group
(-COOH) head at one end and an
attached hydrocarbon chain ("tail").
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XI. Lipids are mostly hydrophobic molecules with
diverse functions LIPIDS A. Fats Hydrocar
bon chain has a long carbon skeleton usually
with an even number of carbon atoms (most
have 16 - 18 carbons). Nonpolar C-H bonds
make the chain hydrophobic and not water
soluble.
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Whats wrong here?
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XI. Lipids are mostly hydrophobic molecules with
diverse functions LIPIDS A. Fats Some
characteristics of fat include Fats
are insoluble in water. The
source of variation among fat molecules
is the fatty acid composition. Fatty
acids in a fat may all be the same, or
some (or all) may differ. Fatty
acids may vary in length.
Fatty acids may vary in number and
location of carbon - to carbon double
bonds (as shown on the next slide) gtgtgt
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XI. Lipids are mostly hydrophobic molecules with
diverse functions LIPIDS A. Fats
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Cushions vital organs in mammals (e.g.
kidney). Insulates against heat loss (e.g.
mammals such as whales and seals).
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XI. Lipids are mostly hydrophobic molecules with
diverse functions LIPIDS B. Phospholipids
Compounds with molecular building blocks
of Glycerol two fatty acids one
phosphate group usually an additional small
chemical group attached to the phosphate.
Differ from fat in that the third carbon
of glycerol is joined to a negatively charged
phosphate group.
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XI. Lipids are mostly hydrophobic molecules with
diverse functions LIPIDS B. Phospholipids
Can have small variable attached to
phosphate. Are diverse depending upon
differences in fatty acids and in phosphate
attachments. Show ambivalent behavior towards
H2O.
Hydrocarbon tails are hydrophobic, and the
polar head (phosphate group with attachments)
is hydrophilic.
Are major constituents of cell membranes.
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Is the precursor to many other steroids
including vertebrate sex hormones and bile
acids. Is a common component of animal cell
membranes.
Can contribute to atherosclerosis.
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A quick LIPID REVIEW gtgtgt
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XII. PROTEINS. PROTEINS A. Overview
A protein is a polymer of amino acids. An
amino acid has a carboxyl end (COOH) and an
amino end (NH2), as well as a variable R
group. Twenty kinds of amino acids are
used in protein structure.
B. Peptides 1. Two amino acids is a
peptide. 2. A peptide bond is formed
between the amino group (NH2) of one amino
acid and the carboxyl group (COOH) of the
next. 3. Peptide
size varies there are dipeptides,
tripeptides, polypeptides.
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XII. PROTEINS. PROTEINS C. Levels
of Protein Structure 1. Primary structure
the order of the amino acids in the
peptide. 2. Secondary structure is a coiled
or folded shape held together by hydrogen
bonds.
3. Tertiary structure is formed by
further bending and folding. 4.
Quaternary structure between two or more
polypeptide chains.
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Not Thebest pict.
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XII. PROTEINS. PROTEINS D. Protein
Conformation and Denaturation. 1. Protein
conformation refers to its overall shape. It
cannot function properly if the shape is
altered. 2. Denaturing a protein using heat
or changes in pH causes it to unwind and
destroys it.
E. Protein Functions. Protein functions
include serving as structural components, for
catalysis as ENZYMES, for communication, to
provide membrane transport, in cell recognition
and protection, and for movement.
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The End
Chapter Summary on pp. 59 - 60 in Text Holes
Tenth Edition
ONLY ATTEMPT THESE WHEN YOU FEEL THAT YOU ARE
READY FOR THE EXAM !!