Molecules of Life

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Chapter 2 Molecules of Life
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• The Atom
• Fundamental unit of matter
• Nucleus
• Protons Positive charge mass of 1
• Neutrons No charge mass of 1
  
• Electrons
• Spin around the nucleus in orbitals (shells)
• Negative charge No mass
• Electrically negative of protons electrons

http//www.yourdictionary.com/ahd/a/a0501900.html
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• Electrons
• Electrons carry energy. How??
• Electrons are negatively charged as such, they
  are attracted to the positive charge in the
  nucleus. Meanwhile, electrons repel other
  electrons.
• REMEMBER OPPOSITES ATTRACT and SAME REPELS
• Electrons spin around the nucleus at various
  levels. They are attracted to the nucleus but
  repel each other, therefore it takes work to keep
  them in orbit.
• Example is an apple in your hand.

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Electron Orbitals

• Volumes of space that surround the
• nucleus
• Electrons move in orbitals

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Electron shells and electron orbitals Constants
The 1st shell in any atom can hold 2
electrons The 2nd shell in any atom can hold 8
electrons The 3rd shell in any atom can hold 8
electrons
Shell of electrons each shell
can hold First shell 2 Second shell
8 Third shell 8
P N
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• Electron Movement
• Electron shells energy levels
• Electron orbital Volume of space around a
  nucleus where an electron is most likely to be
  found
• Useful Analogy
• planets (electrons) ORBITING around the sun
  (nucleus)

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Why is it necessary to understand how electron
orbitals work? This isnt a Chemistry class,
right?? Electrons and the energy they posses
(their energy state) determine the chemical
behavior of atoms thus, the losing, gaining or
sharing of electrons is the BASIS FOR CHEMICAL
REACTIONS IN WHICH CHEMICAL BONDS FORM (chemical
bonds include hydrogen bonding, ionic bonding and
covalent bonding).
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If electrons couldnt lose or gain other
electrons, or share with other electrons,
chemical bonds would NOT form! Example, H2O
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Element a substance that cannot be reduced into a
simpler component substance through a chemical
process
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http//cougar.slvhs.slv.k12.ca.us/pboomer/chemlec
tures/textass2/secondsemass.html
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• How to Read the Periodic Table
• Elements are arranged LEFT to RIGHT and
  TOP to BOTTOM in order of increasing
  atomic mass.
• Rows are arranged in periods Ex. H and He
  are in period 1 C and O are in period 2
• The period number of an element highest energy
  level an electron in that element occupies in an
  unexcited state
• Therefore,
• H and He have 1 electron shell
• C and O have 2 electron shells

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• Columns represent groups and families.
• Each element symbol has 2 numbers listed atomic
  number and atomic mass.

Atomic Number
Number of protons in the nucleus
6
C
12
Atomic Mass
Number of protons and neutrons in the nucleus
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Fig. 3.3
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Carbon

• Carbon Facts
• 6 protons (Atomic is 6)
• 6 neutrons (Atomic mass is 12so, how do you get
  6?)

N Atomic Mass - P

• 6 electrons (Atomic is 6)

• Is the first electron shell full (inactive)?
• Is the second electron shell full?
• How many unpaired orbitals does C have?

Yes
No
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Carbon

• Carbon Facts
• How many chemical bonds can Carbon form with
  other atoms?

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Can an element ever have a variable number of
neutrons?
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• Isotopes
• Same atom but with a different of neutrons,
  thus a different atomic mass
• Atomic number protons in the nucleus
• Atomic mass protons neutrons
• Having a different number of neutrons in the
  nucleus DOES NOT change the chemical properties
  of an element BUT it DOES change the stability of
  the element!!

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Isotope
Atomic protons protons protons
6 6
6
Atomic Mass P N P N P
N 6 6 12 6 7 13 6 8
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• Medical Uses of Radioactive Isotopes
• Short-lived isotopes are used clinically to
  diagnose pathological abnormalities/disease
• Ex. Use of 99Tc for renal scan
• 99 Tc (tracer) is introduced through your
  bloodstream
• Kidney cells take up the radioactive tracer
  (isotope of Tc 99Tc)
• A camera detects emissions from the tracer and
  records them.
• What makes 99Tc specific for kidney cells?

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The isotope is specific for a protein unique to
kidney cells. Remember, electrons are the basis
for chemical reactions!! So if 99Tc has a
different number of neutrons in its nucleus, the
stability of the electrons in the other shell of
that 99Tc atom are changed. There are 43
isotopes of Technitium! It just so happens that
the particular stability of 99Tc seeks to form a
chemical bond with this unique kidney protein.
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• Matter
• Any substance in the universe that has mass and
  occupies space
• Matter is transformed through chemical bonding
• Conservation of Matter Matter cannot be
  created or destroyed but it can be transformed
• Use of an equation to show how matter is
  transformed
• Reactants Products
• Sodium Chloride Sodium chloride Na
  Cl- NaCl

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• Important Bonds in Biological Membranes
• Way in which atoms link to one another to form
  molecules
• Links are formed through the exchange of
  electrons
• Atoms are driven to react to become more stable
• Atomic stability is achieved by filling an outer
  electron shell
• Non-reactive elements have full outer shells
  INACTIVE
• Types of chemical bonding
• Ionic bonding
• Covalent bonding
• Hydrogen bonding

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• Ionic Bonding
• Creates ions (charged atoms) one atom loses
  electrons and becomes a () charged ion while
  another gains electrons and becomes (-) charged
• Note in charged atoms, the of protons DOES NOT
  equal the of electrons!!!! Protons
  Electrons
• Formed when atoms are attracted to each other by
  opposite electrical charges (i.e. magnet)
• Two key properties of ionic bonding
• They are strong bond (although NOT the strongest)
• They are non-directional

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Ionic Bonding Example Table salt Reactants
Sodium atom has 1 lone electron in its outer
orbital (Ax) Chloride atom has 7
electrons in its outer orbital (Ax) Products S
odium ION that has given up an electron from its
outer shell Chloride ION that has
accepted an electron from Sodium and has included
it in its outer shell
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Fig. 3.8
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Both the sodium ion and the chloride ion are
electrically attracted because of the opposite
charges incurred by the altered electron
orbitals. This electrical attraction results in
the formation of an elaborate matrix resulting in
a crystal of table salt.
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• Covalent Bonds
• Electrons are shared between atoms
• Two key properties of covalent bonding
• VERY STONG!!! (strongest type of bond)
• Directional
• Carbon ALWAYS forms a covalent bond!!!!!
• 2 types
• Non-polar Covalent electrons are equally shared
• Generates hydrophobic molecules (water hating)
• Polar Covalent electrons are unequally shared
• Generated hydrophilic bonds (water loving)

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Non-Polar Covalent Bond Methane (CH4)
H
H
H
H
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Non-Polar Covalent Bond Methane (CH4)
H
H
H
H
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Polar Covalent Bonding H2O
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• Hydrogen Bonding
• Links a polar covalent molecule to another polar
  covalent molecule
• Results in VERY WEAK bonding BUT because so many
  are formed, the complex as a whole is VERY STONG

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Hydrogen Bonding
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• Solutions
• A homogenous mixture of 2 or more substances
• Solute ingredient being dissolved
• Solvent substance that does the dissolving
• Example. You make a solution of water and salt.
  Which is the solute and which is the solvent?

Solute Salt
Solvent Water

• Components of solutions Acids Bases
  Salts pH

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• Components of Solutions, continued
• Acids
• A substance that puts hydrogen ions (H )into a
  solution
• Example Hydrochloric Acid placed in water
• HCl H2O Cl- H
• Water HCl dissolved in water

H
H
H
H
H
H
H
H
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• Components of Solutions, continued
• Bases
• A substance that puts hydroxide ions (OH-) into
  solution
• Example Sodium Hydroxide dissolved in water
• NaOH H2O Na OH-
• Water NaOH dissolved in water

OH
OH
OH
OH
OH
OH
OH
OH
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• Components of Solutions, continued
• Salts
• A substance that puts other ions into solution
  (ions other than H and OH-)
• Example Sodium chloride dissolved in water
• NaCl H2O Na Cl- H2O

Cl
Na
Na
Na
Cl
Cl
Cl
Na
Cl
Na
Na
Na
Cl
Cl
Cl
Na
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• Salts are formed when acids and bases are added
  to each other this results in neutralization of
  the acid and base.
• HCl NaOH NaCl H2O
• (Acid) (Base) (Salt) (Water)

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• Components of Solutions, continued
• pH
• A logarithmic scale that measures the acidity of
  alkalinity (basicity) of a solution
• Note the difference between 2 units on the pH
  scale is 10, therefore, the difference between 3
  pH units is

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• pH scale
• Neutral pH 7
• Acidic pH lt 7
• Basic pH gt 7

• Buffers keep pH within normal limits

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pH scaleAcidicNeutralBasic
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• The Importance of Water to Life
• Three quarters of the Earths surface is water
• Two thirds of the human body is composed of water
• All organisms require water
• Since water is an essential part of life, its
  surprising that the bond that 2 atoms of H make
  with 1 atom of O is so weak. Actually, the bond
  that forms a single H20 molecule (which is what
  type of bond??) lasts only 1 / 100,000,000,000 of
  a second!
• However, water molecules form extensive lattices
  with other water molecules. This occurrence leads
  to the important physical properties of water!

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• Water
• Water is a polar covalently bonded molecule that
  forms hydrogen bonds with other polar covalently
  bonded water molecules.
• Universal solvent
• Ice (solid water) is less dense than liquid ice.
• Ex. Ice floats in liquid water
• 4. Water has a high capacity to store heat. Water
  stabilizes Earths temperature (Remember, water
  comprises ¾ Earths surface.
• 5. Adhesion and cohesion

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• Properties of Water
• Bonds to hydrophilic substances and repels
  hydrophobic ones
• Stabilizes temperature
• Expands when it freezes
• Cohesive
• Dissolves substances

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Cohesion
Since water is polar, it is attracted to other
polar molecules. Cohesion occurs when the other
polar molecule is water. Surface Tension Created
by cohesion and due to the strong hydrogen
bonding between the polar water molecules.
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ChemistryMacromolecules
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• Forming Macromolecules
• Organic molecule
• Formed by living organisms
• Carbon-based core with functional groups attached
• Functional group
• Groups of atoms with special chemical properties
• Confer specific chemical properties on the
  molecules that posses them
• Ex.
• Macromolecules
• Potentially large molecules (Macro-) that are the
  building materials of cells. They are the
  material that makes up the body of cells and the
  machinery that runs within cells
• Thousands of different types in an organism BUT
  the body is made of 4 types (protein, nucleic
  acid, carbohydrates, lipids)

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Five Principle Functional Groups Figure 3.17
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More on Macromolecules

• Polymer a molecule made of MANY chains of a
  similar subunit
• Monomer a single molecule that is the BASIC
  building block of a macromolecule
• Monomers can combine to form a polymer
• View animation on Polymer formation
  http//science.nhmccd.edu/biol/dehydrat/dehydrat.h
  tml

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Dehydration Synthesis

• The process of FORMING a macromolecule
• Forms a COVALENT bond between two subunits
• A hydroxyl (OH) group is removed from one subunit
• A hydrogen (H) is removed from the other subunit

• Small molecule small molecule large
  molecule H20
• View animation

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• Hydrolysis Reactions
• The BREAKING up of a polymer
• Adds a water molecule (H20)
• H20 comes in and
• A hydrogen becomes attached to one subunit
• A hydroxyl (OH) becomes attached to the other
  subunit
• Results in the BREAKING of the covalent bond that
  previously held the macromolecule (polymer)
  together
• Large molecule H20 2 small molecules
• View animation

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Carbohydrates

• Contain C, H, O atoms (121 ratio)
• Carbon atoms Oxygen atoms
• Hydrophilic
• Excellent for energy storage
• Why?? The C-H bonds store energy. When an
  organism requires an energy source, C-H bonds are
  the ones most often broken. This results in the
  release of stored energy.
• Comprise 1-2 of a cells mass
• 2 types simple carbohydrates
• complex carbohydrates

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Simple Carbohydrates

• Monosaccharide
• Simple sugar
• Consists of one subunit smallest carbs
• Ex. Glucose (C6H12O6)
• Also, fructose, ribose, deoxyribose
• See Figure 3.29
• Disaccharide
• Result of linkage of two monosaccharides
• Ex. Sucrose, lactose, maltose
• See Figure 3.30

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Complex Carbohydrates

• Polysaccharides
• Long chain polymers of sugars
• The body converts soluble sugars into insoluble
  forms (polysaccharides). These polysaccharides
  are then deposited throughout the body in
  specific storage areas.
• Preferred form of energy storage
• Plants starch glucose polysaccharide that
  plants use to store energy
• Animals glycogen highly insoluble
  macromolecule formed of glucose and
  polysaccharides that serves as stored energy

• Utilized by plants and animals as structural
  polysaccharides (chitin and cellulose) linkage
  is unique such that the chains are not recognized
  by enzymes that normally break polysaccharide
  bonds.

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Lipids

• Contain C, H, and O
• Hydrophobic (held together by non-polar covalent
  bonds)
• Used as long term storage
• Contains MORE energy-rich C-H bonds than carbs

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LipidsI. Triglycerides (Fat)

• Fats are synthesized from 2 components
• 1. Fatty acid long chain C and H atoms ending
  in a COOH group
• 2. Glycerol a three C molecule note, glycerol
  is an alcohol
• Glycerol forms a backbone to which 3 fatty acids
  are attached via a dehydration reaction
  fat molecule
• Provides long term energy storage, insulation

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Lipids, continuedTriglycerides

• Saturated
• Fatty acids with ALL internal carbon atoms
  forming covalent bonds with two hydrogen atoms
• Animal source
• Solid at room temperature and body temp (37C)
• Unsaturated
• Fats with fatty acids that have double bonds
  between 1 or more pairs of carbon atoms
• Plant source
• Kink imparts a 30 bend
• Liquid at room temperature Low melting point

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Why are unsaturated fats good while saturated
fats are bad for your health?

• The C C bond in unsaturated fats creates a
  negative charge that causes the fat molecules to
  repel each other rather than stick together (as
  they do in long chain saturated fats).

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Hydrogenation

• Example Margarine
• Margarine is formed from heating oil (unsaturated
  triglycerides) in the presence of a metal
  catalyst (aluminum) and hydrogen. That
  environment breaks the C C and replaces it
  with two hydrogen atoms producing very hard,
  saturated fats. Chemists vary the degree of time
  that hydrogenation occurs resulting in a product
  that is soft and spreadable (partially
  hydrogenated).
• N.B. Margarine is 10-50 trans fatty acids BAD
• Margarine has been found to be contaminated
  with aluminum. Al is a causative agent in AD

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What is a trans-fatty acid?

• Trans fatty acids have hydrogen atoms on opposite
  sides of the double bonded carbons
• Cis fatty acids have hydrogen atoms that on the
  same side with each other
• The enzymes that metabolize fat can only
  metabolize cis fatty acids

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Butter is a saturated triglyceride.Why does
butter soften as it melts, why doesnt it
instantly melt?

• Because the fatty acid chains that come off
  the glycerol backbone differ. Each different
  fatty acid has a different melting point.

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Common fats

• Saturated
• Palmitic acid
• Unsaturated
• Omega-3

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Types of Lipids

• II. Phospholipid
• Glycerol 2 fatty acids phosphate group
• Polar group at one end (glycerol and phosphate)
  and highly nonpolar group at other end (fatty
  acid tails)
• Ex. Cell membrane
• III. Steroid
• 4-interlocking rings
• Found in cell membranes
• Ex. Cholesterol, hormones

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Basic structure of a triglyceride
Basic structure of a phospholipid
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Phospholipid Bilayer
Hydrophobic
Hydrophilic
Hydrophobic
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Protein

• Comprises 10-30 cell mass
• Functional roles (enzymes) and structural roles
  (collagen, keratin)
• All proteins are a long polymer chain of amino
  acid subunits
• small molecules, 20 total
• all 20 have a basic structure of a central carbon
  atom to which the 4 following are
  attached hydrogen atom
• amino group (-NH2)
• carboxyl group (-COOH)
• an R group

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Amino Acids
Nonpolar Hydrophobic
Polar Uncharged Hydrophilic
Polar Ionizable (Acidic) Hydrophilic
Polar Ionizable (Basic) Hydrophilic
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How to make a protein

• Link specific amino acids together in a
  particular order
• Peptide bond covalent bond that links 2 amino
  acids together
• Polypeptides long chains of amino acids liked
  by peptide bonds

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Protein Structure

• Structure determines function
• What determines protein structure?

Amino acid sequence of the protein
Four levels of protein structure Primary Second
ary Tertiary Quaternary
All levels of protein structure are ultimately
determined by amino acid sequence!!
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Primary Structure of Protein

• The sequence of amino acids of a polypeptide chain

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Secondary Structure of a Protein

• Initial folding of the polypeptide chain caused
  by formation of hydrogen bonds
• Can result in sheets (Beta sheets) or coils
  (alpha helices) of polypeptides
• Because some AAs are polar and some are nonpolar,
  a polypeptide folds in solution nonpolar regions
  are forced together (forced by the polar groups
  and their attraction to water resulting in the
  polar groups repulsion of nonpolar amino acids)

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Tertiary Structure of a Protein

• A folded and twisted molecule
• Repulsion by water forces nonpolar amino acids
  towards the interior leaving polar amino acids
  exposed to the exterior

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Quaternary Structure of a Protein

• Spatial arrangement of several component
  polypeptide chains

http//www.chemsoc.org/exemplarchem/entries/2004/d
urham_mcdowall/images/1a3n-4-struct.png
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Denaturation

• What influences how a polypeptide folds in
  solution?

The polar nature of the environment When the
polar nature of the environment changes (? temp
or ? pH), hydrogen bonding may be altered which
may then cause unfolding of the protein, or
denaturation.

• Ex. Frying an egg

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Nucleic Acids

• Long polymers of nucleotides that serve as
  information storage devices of cells
• Nucleotides have 3 components
• A five carbon sugar
• A phosphate group (PO4)
• An organic nitrogen-containing base

• Polynucleotide chains
• - Chain of nucleic acids in which sugars are
  linked in a line by the phosphate groups
• SUGAR P SUGAR P - SUGAR P

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Nucleic Acids

• DNA and RNA
• DNA (deoxyribonucleic acid)
• Possible nucleotides Adenine, Guanine, Cytosine,
  THYMINE
• Structure 2 nucleotide strands double helix
• RNA (ribonucleic acid)
• Possible nucleotides Adenine, Guanine, Cytosine,
  URACIL
• Long, single strand
• How do nucleic acids function as information
  storage devices?
• Each nucleotide serves as a letter and each
  nucleic acid has different nucleotides (letters)

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Nucleotides
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• Everyday Science
• Lactose Intolerance the inability to digest
  foods containing milk due to a lack of the
  lactase enzyme (enzyme, a protein that disrupts
  chemical bonds in other molecules allowing
  reactions to occur or preventing their
  occurrence).
• Normally, milk sugar (lactose) is digested by the
  lactase enzyme. Lactase binds to lactose in milk
  and breaks the chemical bonds that are
  responsible for holding the sugar together. This
  allows the broken down sugars to pass through the
  bloodstream and be utilized by the body.
• LI people lack the lactase enzyme, thus they
  cannot digest milk protein. This leads to a
  buildup of leading to nausea, cramps and
  bloaing.

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Normal Lactose Metabolism
AB
Milk Protein Lactase Lactose
Glucose Galactose Glucose
_____Galactose Bloodstream
GI tract
Energy
LI symptoms
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• Questions
• What is the strongest type of single bonded
  molecule?

Covalent bond (both polar and non-polar types)
2. Isotopes have a different measure of stability
when compared to their parent element on the
periodic table. True or False
True
3. You can determine the number of neutrons
present in an atom by subtracting the number of
protons from the ____.
Atomic mass
4. When preparing a solution, you accidentally
add too much of an acidic component. This creates
an excess of _____. The desired pH is 8 the pH
you measure is 6. You decide that it shouldnt
make too much of a difference, youre only 2
units off. What is wrong with this logic?
H, or Hydrogen ions
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A difference of 2 units on the pH scale
correlates to a 100 fold more acidic solution.
Therefore, your solution has 100 times more
Hydrogen ions then the desired solution
concentration.
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• Websites for additional info from todays
  lecture
• www.webelements.com Interactive periodic table
• http//web.buddyproject.org/web017/web017/pertab.h
  tml