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Molecules of Life

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Title: Molecules of Life


1
Chapter 2 Molecules of Life
2
  • 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
3
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4
  • 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.

5
Electron Orbitals
  • Volumes of space that surround the
  • nucleus
  • Electrons move in orbitals

6
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
7
  • 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)

8
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).
9
If electrons couldnt lose or gain other
electrons, or share with other electrons,
chemical bonds would NOT form! Example, H2O
10
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11
Element a substance that cannot be reduced into a
simpler component substance through a chemical
process
12
http//cougar.slvhs.slv.k12.ca.us/pboomer/chemlec
tures/textass2/secondsemass.html
13
  • 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

14
  • 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
15
Fig. 3.3
16
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
4
17
Carbon
  • Carbon Facts
  • How many chemical bonds can Carbon form with
    other atoms?

4
Can an element ever have a variable number of
neutrons?
18
  • 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!!

19
Isotope
Atomic protons protons protons
6 6
6
Atomic Mass P N P N P
N 6 6 12 6 7 13 6 8
14
20
  • 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?

21
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.
22
  • 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

23
  • 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

24
  • 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

25
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
26
Fig. 3.8
27
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.
28
  • 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)

29
Non-Polar Covalent Bond Methane (CH4)
H
H
H
H
30
Non-Polar Covalent Bond Methane (CH4)
H
H
H
H
31
Polar Covalent Bonding H2O
32
  • 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

33
Hydrogen Bonding
34
  • 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

35
  • 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
36
  • 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
37
  • 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
38
  • 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)

39
  • 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

100
  • pH scale
  • Neutral pH 7
  • Acidic pH lt 7
  • Basic pH gt 7
  • Buffers keep pH within normal limits

40
pH scale Acidic Neutral Basic
41
  • 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!

42
  • 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

43
  • Properties of Water
  • Bonds to hydrophilic substances and repels
    hydrophobic ones
  • Stabilizes temperature
  • Expands when it freezes
  • Cohesive
  • Dissolves substances

44
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45
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.
46
Chemistry Macromolecules
47
  • 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)

48
Five Principle Functional Groups Figure 3.17
49
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

50
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

51
  • 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

52
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

53
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

54
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.

55
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

56
Lipids I. 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

57
Lipids, continued Triglycerides
  • 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

58
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).

59
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

60
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

61
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.

62
Common fats
  • Saturated
  • Palmitic acid
  • Unsaturated
  • Omega-3

63
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

64
Basic structure of a triglyceride
Basic structure of a phospholipid
65
Phospholipid Bilayer
Hydrophobic
Hydrophilic
Hydrophobic
66
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

67
Amino Acids
Nonpolar Hydrophobic
Polar Uncharged Hydrophilic
Polar Ionizable (Acidic) Hydrophilic
Polar Ionizable (Basic) Hydrophilic
68
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

69
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!!
70
Primary Structure of Protein
  • The sequence of amino acids of a polypeptide chain

71
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)

http//kvhs.nbed.nb.ca/gallant/biology/biology.htm
l
72
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

73
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
74
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

75
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

76
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)

77
Nucleotides
78
  • 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.

79
Normal Lactose Metabolism
AB
Milk Protein Lactase Lactose
Glucose Galactose Glucose
_____Galactose Bloodstream
GI tract
Energy
LI symptoms
80
  • 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
81
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.
82
  • Websites for additional info from todays
    lecture
  • www.webelements.com Interactive periodic table
  • http//web.buddyproject.org/web017/web017/pertab.h
    tml
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