Download Slide 1

Chapter 2
Molecules of Life
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
http://www.yourdictionary.com/ahd/a/a0501900.html
•Electrically negative: # of protons = # electrons
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.
• Volumes of space that surround the
•nucleus
• Electrons move in orbitals
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
P+N
# of electrons
each shell can
hold
First shell
2
Second shell
8
Third shell
8
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)
Why is it necessary to understand how electron orbitals
work? This isn’t 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).
If electrons couldn’t lose or gain other electrons, or
share with other electrons, chemical bonds would NOT
form!
Example, H2O
Element
a substance that cannot be reduced into a simpler component
substance through a chemical process
http://cougar.slvhs.slv.k12.ca.us/~pboomer/chemlectures/textass2/secondsemass.html
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
•Columns represent groups and families.
•Each element symbol has 2 numbers listed: atomic
number and atomic mass.
Atomic Number
6
C
Number of protons in the
nucleus
12
Atomic Mass
Number of protons and
neutrons in the nucleus
Fig. 3.3
Carbon
Carbon Facts:
•6 protons (Atomic # is 6)
•6 neutrons (Atomic mass is
12…so, how do you get 6?)
N = Atomic Mass - P
•6 electrons (Atomic # is 6)
•Is the first electron shell full (inactive)? Yes
•Is the second electron shell full? No
•How many unpaired orbitals does C have? 4
Carbon
Carbon Facts:
•How many chemical bonds
can Carbon form with other
atoms?
4
Can an element ever have a
variable number of neutrons?
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!!
Isotope
Atomic #
# protons
6
Atomic Mass
#P+#N
# protons
# protons
6
6
#P + # N
#P+#N
6 + 6 = 12
6 + 7 = 13
6 + 8 = 14
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?
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.
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
•Sodium + Chloride
Na+ + Cl-
Products
Sodium chloride
NaCl
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
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
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:
Sodium 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
Fig. 3.8
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.
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”)
Non-Polar Covalent Bond: Methane (CH4)
H
H
H
H
Non-Polar Covalent Bond: Methane (CH4)
H
H
H
H
Polar Covalent Bonding: H2O
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
Hydrogen Bonding
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
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
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
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
Cl
Na Cl
Na
Cl
•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)
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 < 7
•Basic : pH > 7
•Buffers keep pH within normal limits
Acidic
Neutral
Basic
The Importance of Water to Life
•Three quarters of the Earth’s 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, it’s 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!
Water
1. Water is a polar covalently bonded molecule that forms
hydrogen bonds with other polar covalently bonded
water molecules.
2. Universal solvent
3. 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
Earth’s temperature (Remember, water comprises ¾
Earth’s surface.
5. Adhesion and cohesion
Properties of Water
•Bonds to hydrophilic substances and repels
hydrophobic ones
•Stabilizes temperature
•Expands when it freezes
•Cohesive
•Dissolves substances
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.
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)
Five
Principle
Functional
Groups
Figure 3.17
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.html
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
•
View animation
large molecule + H20
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
•View animation
2 small molecules
Carbohydrates




Contain C, H, O atoms (1:2:1 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
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
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.
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
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
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
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).
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
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
Butter is a saturated triglyceride.
Why does butter soften as it melts, why
doesn’t it instantly melt?
Because the fatty acid chains that come off the glycerol
backbone differ. Each different fatty acid has a
different melting point.
Common fats
 Saturated
 Palmitic acid
 Unsaturated
 Omega-3
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
Basic structure of a triglyceride
Basic structure of a phospholipid
Phospholipid Bilayer
Hydrophobic
Hydrophilic
Hydrophobic
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
Amino Acids
Nonpolar
Hydrophobic
Polar
Uncharged
Hydrophilic
Polar
Ionizable
(Acidic)
Hydrophilic
Polar Ionizable (Basic)
Hydrophilic
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
Protein Structure
 Structure determines function
 What determines protein structure?
Amino acid sequence of the protein
Four levels of protein structure:
Primary
Secondary
Tertiary
Quaternary
All levels of protein structure are ultimately determined by
amino acid sequence!!
Primary Structure of Protein
 The sequence of amino
acids of a polypeptide
chain
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.html
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
Quaternary Structure of a Protein
 Spatial arrangement of
several component
polypeptide chains
http://www.chemsoc.org/exemplarchem/entries/2004/durham_mcdowall/images/1a3n-4-struct.png
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
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 …
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)
Nucleotides
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.
ABNormal Lactose Metabolism
Milk
Protein
Lactase
Lactose
Glucose +
Galactose
Glucose _____Galactose
GI tract
LI symptoms
Bloodstream
Energy
Questions
1. 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 shouldn’t make too much of a difference,
you’re only 2 units off. What is wrong with this logic?
H+, or Hydrogen ions
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.
•Websites for additional info from today’s lecture:
www.webelements.com Interactive periodic table
http://web.buddyproject.org/web017/web017/pertab.html