Transcript The Chemistry of Life

The Chemistry of Life
Basic Chemistry
Matter

has mass & takes up
space
Elements



25 required for life
C,H,O,N – make up
96% of living things
P,S,Ca,K – most of
the remaining 4%
Trace Elements



Required but only in
minute amounts
Some required by all
living things – Fe
Others required only
by certain species –
Iodine only for
vertebrates
Goiters caused by iodine
deficiency
www.pipevet.com/photos/goiter.htm
The thyroid gland requires iodine to produce one of it’s hormones.
Without iodine, the gland swells. Iodized salt provides enough
iodine to prevent this condition.
Atoms
Smallest units of
matter
Composed of
protons (+) and
neutrons in nucleus
and electrons (-) in
orbitals
www.phschool.com
Periodic Table Information
Atomic Number


Represents # of
protons
Also # of electrons in
a stable atom of an
element
Atomic Mass
Sum of protons & neutrons
 Electron mass is small and
almost negligible

www.sparknotes.com
Unstable Atoms
Ions




Different # of
electrons
Atoms with a charge
More electrons &
charge is negative
Less electrons &
charge is positive
Isotopes
Different # of neutrons
 Often radioactive
 Used as diagnostic tracers
 EX: barium, iodine

** The number of protons does
not change! This would create
an entirely different element.
Diagnostic Tracers
http://student.bmj.com/issues/03/10/education/358.php
www.nature.com/gimo/contents/pt1/full/gimo29.html
Bonding
Atoms bond in order to fill their valence
shell (outer energy level)
Octet Rule
The idea that most atoms want 8 electrons
in their outer shell and will share, steal, or
give away electrons in order to fill the
valence shell
 Exceptions are those who have less than 6
total electrons

Covalent Bonding
Valence electrons (outer shell) are
shared
Form molecules
Single, double or triple bonds are
possible
www.school-for-champions.com
Types of Covalent Bonds
Nonpolar Covalent


Electrons are shared
equally
EX: O2
academic.brooklyn.cuny.edu
Polar Covalent


Electrons are not
shared equally
The more
electronegative atom
exerts a greater pull
on the electrons being
shared
 EX: H2O
Ionic Bonding
Electrons are lost or gained from the
outer shell in order to fulfill the octet rule
www.school-for-champions.com
Hydrogen Bonding
Weak bonds
formed between
molecules that
contain polar
covalent bonds
Bonding animation:
http://trc.ucdavis.edu/biosci10v/bis10v/media/ch02/bond_types.html
www.biology.arizona.edu
Molecular
Structure vs. Function
Each molecule has a characteristic size
& shape which determine its function
endorphins are brain signal molecules that
fit into specific receptors used in pain
suppression & euphoria.
 Morphine & heroin mimic the shape of
endorphins and produce similar effects
when they bind to receptors

Endorphin molecule
http://www.bio.davidson.edu/Courses/anphys/1999/Self/Ligands.htm
www.charisma.org.uk/neuron-p.gif
Morphine molecule
Earth’s Biological Medium
Polarity
Slight charge on either end of the
molecule due to the unequal
electronegativities of hydrogen &
oxygen
This leads to many other
properties…
Cohesion
www.biology.arizona.edu
http://www.arroyoseco.org/conservation.htm
Adhesion
en.wikivisual.com
www.ccs.k12.in.us
Surface Tension
news.bbc.co.uk/.../photo_galleries/4670308.stm
http://faculty.vassar.edu/suter/1websites/bejohns/mateselection/files/female.htm
www.ext.vt.edu
Specific Heat
Amount of heat that must be
absorbed or lost for 1g of a
substance to change by 1oC
Water has high specific heat – it
resists temperature change
This keeps the earth
within viable temperature
limits.
www.michigan.org
Evaporative Cooling
AP Photo/Darin Cummings
www.doggonesafe.com/dog%20communication.htm
Density of Ice
www.astrobiology.com/lter/album01/179.html
Solid water is less dense
than its liquid because as
hydrogen bonds freeze,
they force molecules
further apart
In large bodies of water, a
top layer of ice actually
insulates the water below
4oC is when water is at its
most dense
http://www.astrobiology.com/lter/album01/209.html
Universal Solvent
Water dissolves many materials
creating aqueous solutions (water is
solvent, what’s being dissolved is
solute)
This property is the direct result of
water’s polar structure
Hydrophilic – substances attracted to
water
 Hydrophobic – repel water (or not
attracted)

Water & pH
In pure water, even if dissociation
occurs, the concentration of H+ and
OH- ions is equal
When acids or bases are added to
water, these concentrations change
quickly
pH is a measure of hydrogen ion
concentration on a scale between 014
Acids
Chemical compounds that donate H+
ions as they dissociate in solution

EX: HCl  H+ Cl-
The more acidic a solution,
The higher the H+ concentration
 The lower the pH

Taste sour
pH < 7
www.elmhurst.edu
Bases
Compounds that accept H+ ions and
remove them from solution
Some donate OH- ions
The more basic a solution,
The lower its H+ concentrationwww.chemistryland.com
 The higher its pH value

Taste bitter
community.tvguide.com
Buffers
Substances that resist changes in pH
Many of these in the body since even
minor changes can be life threatening

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
EX: blood ph is 7.4
CO2 (carbonic acid when dissolved in water)
donates H+ to lower pH
HCO3 (bicarbonate) binds excess H+ to raise
pH
I am H2O
Organic Compounds
Functional Groups
Parts of organic compounds most
commonly involved in chemical
reactions
Determine what bonds will be formed
and functions of specific compounds
(Structure/Function)
Functional Groups
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
Organic Compounds
All the compounds found in living
things that contain CARBON
These compounds are divided into 4
families:
Carbohydrates
 Lipids
 Proteins
 Nucleic Acids

1. Carbohydrates
Their main function is to provide energy
Examples of “carbs” include candy,
sugar, pasta, bread, etc.
All contain hydroxyl & carbonyl groups
There are 3 groups of carbohydrates:
1.
2.
3.
Monosaccharides
Disaccharides
Polysaccharides
A. Monosaccharides
Mono = single or simple
Saccharide = sugar
These are simple sugars
Examples are glucose & fructose
Monosaccharides always have the
formula CH2O (they are a hydrate of
Carbon)

EX: glucose formula is C6H12O6
Glucose Structure
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
Examples of Monosaccharides
Research
Researchers have found new evidence that soft drinks sweetened with
high-fructose corn syrup (HFCS) may contribute to the development of
diabetes, particularly in children. In a laboratory study of commonly
consumed carbonated beverages, the scientists found that drinks
containing the syrup had high levels of reactive compounds that have
been shown by others to have the potential to trigger cell and tissue
damage that could cause the disease, which is at epidemic levels.
HFCS is a sweetener found in many foods and beverages, including nondiet soda pop, baked goods, and condiments. It is has become the
sweetener of choice for many food manufacturers because it is
considered more economical, sweeter and more easy to blend into
beverages than table sugar. Some researchers have suggested that highfructose corn syrup may contribute to an increased risk of diabetes as
well as obesity
B. Disaccharides
Double sugars
These are things like sucrose, lactose, and
maltose
They are formed by removing a water to bond
monosaccharides together
Glycosidic linkage - bond formed between
monosaccharides
Dehydration Synthesis
Dehydration Synthesis
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
Monomers   Polymers
http://universe-review.ca/I11-10-reactions.jpg
C. Polysaccharides
Complex sugars
Breads, pastas
We break these down in order to get
energy in our body. Water must be
added to bust these apart –
Hydrolysis
Hydrolysis
www.biotopics.co.uk/as/disaccharidehydrolysis.gif
Indicators of Carbohydrates
biology.unm.edu
Benedicts Solution
Turns from blue to orange in
a MONOSACCHARIDE

Iodine

Turns from amber to black in a
POLYSACCHARIDE
iws.ccccd.edu
2. Lipids
Hydrophobic - little or no affinity for
water
Smaller than true polymers
Highly varied in form & function
Types of lipids include
A.
B.
C.
D.
Fats
Phospholipids
Steroids
Waxes & oils
A. Fats
Monomers
Glycerol
 Fatty acids

Ester linkage - bond between fatty acids &
glycerol formed by dehydration synthesis
Function in energy storage & protection
Dehydration Synthesis of a fat3 waters removed between
hydroxyl of glycerol and
carboxyl of fatty acid to form
ester linkages
io.uwinnipeg.ca/~simmons/cm1503/Image76.gif
Saturated vs. Unsaturated Fats
Saturated
Solids @ room
temp
 Animal fats
 Build up inside
vessels
 No double bonds
between carbons
(saturated with
hydrogens)

Unsaturated
Liquids @ room
temp
 Plant oils
 Double bonds
between carbons
(do not have max
# of hydrogens

Unsaturated vs. Saturated
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
FATS
Which of these are saturated?
B. Phospholipids
Similar to fats but with only 2 fatty acids
rather than 3
The 3rd hydroxyl group of glycerol is
joined to a phosphate group
Ambivalent behavior toward water
Lipid tails are hydrophobic
 Phosphate heads have – charge and are
hydrophilic

Major component of cellular membranes
Phospholipids
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/phospc.gif
www.biologycorner.com/resources/lipidbilayer.gif
C. Steroids
Carbon skeleton of 4 fused rings
Used in animal cell membranes &
hormones
Extreme levels in the bloodstream may
contribute to atherosclerosis
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookCHEM2.html
3. Proteins
Monomers – amino acids
Contain both amino & carboxyl groups
Sophisticated in both structure &
function
Used in support, storage, transport,
signaling, immunity, metabolism
Account for more than 50% of dry
weight of cells
Peptides
Peptides


Individual amino
acids OR
sequence of 2 or
more amino acids
created by
dehydration
synthesis
Peptide bond –
between amino
acids
ghs.gresham.k12.or.us
Proteins
One or more polypeptides folded and
coiled into specific conformations
www.biosci.ohio-state.edu
Levels of Protein Structure
Primary Structure (1o)
Unique sequence of amino acids
 EX: Hemoglobin – normal vs. sickled
 EX: Insulin

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG
Secondary Structure (2o)
Initial coiling and folding patterns that result
from hydrogen bonds
 EX: alpha helix – coils (alpha keratin in hair)
 EX: pleated sheet – folds (silk proteins of
insects & spiders

http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG
Tertiary Structure (3o) – secondary coiling
and folding
Quaternary Structure (4o) – overall protein
structure that comes from the way all the
polypeptide subunits are situated
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/prot_struct-4143.JPG
Protein Structure
Conformation & structure of proteins can
be affected by pH, salt concentration,
temperature and other environmental
factors.
If the shape of a protein is changed, it is
DENATURED and becomes inactive.
Enzymes
Proteins that lower the amount of activation
energy needed to start reactions
Catalysts that speed up reactions without
being consumed or changed by the reaction
Has a specific active site that fits a specific
substrate
Rate at which they work depends on things
like temperature, pH, amount of substrate
and amount of enzyme present
Metabolism, Energy &
Enzymes
Chapter 6
Metabolism
The total amount of an organism’s
chemical processes and reactions
Metabolism = catabolic + anabolic
reactions
Catabolic Reactions
Chemical reactions that break down
molecules
Release energy

EX: cellular respiration where glucose is
broken down and ATP is released
Anabolic Reactions
Reactions that build complex molecules
from simpler ones
Requires energy input

EX: synthesis of proteins from amino acids
Energy Transformations
1st Law of Thermodynamics

Energy can be transferred and
transformed, but it can be neither created
nor destroyed ~ Conservation of Energy
2nd Law of Thermodynamics

Every energy transfer makes the universe
more disordered (Entropy)

EX: heat is energy in its most random state
Free Energy
Portion of a system’s energy that can
perform work when temperature is
uniform throughout the system
“free” because its available for work
Represented by G
Energy Reactions
Exergonic Reaction
Has a release of free energy
- ΔG
 Catabolic reactions are also exergonic


EX: cellular respiration
Endergonic Reaction
Absorbs free energy
+ΔG
 Anabolic reactions are also endergonic


EX: photosynthesis
Cellular Work
3 main kinds of work done by a cell
1. Mechanical
Movement
EX: muscle contraction; cilia beating
2.
Transport
Pumping of substances across membranes
3.
Chemical
Pushing of endergonic reactions that d not occur
spontaneously
EX: dehydration synthesis
ATP
Adenosine TriPhosphate




Energy molecule used to power cellular work
Adenine, ribose sugar & 3 phosphate groups
Hydrolysis of the last phosphate group causes the
release of free energy
Renewable molecule regenerated by the addition
of a phosphate group to ADP (phosphorylation)
ATP Animation
www.theory-of-evolution.net
biology.clc.uc.edu
www.biochem.arizona.edu
Inhibition
Competitive Inhibition

When another molecule competes directly
for the active site of an enzyme and blocks
it so the substrate cannot attach
Noncompetitive Inhibition
When a molecule attaches to the enzyme
somewhere other than the active site
 This changes the shape of the active site
preventing attachment to the substrate

4. Nucleic Acids
Store & transmit hereditary information
EX: DNA & RNA
 Monomers are nucleotides
 Each nucleotide contains a sugar,
phosphate group and nitrogen base (A, T,
G, C)
 Sugars –

http://www.csb.yale.edu/userguides/graphics/ribbons/help/dna_rgb.html
DNA has deoxyribose sugars
 RNA has ribose sugars
