Download Chemical Basis of Life

Chemistry of Life
Ch. 2 and 3
If you tear paper in half, and keep
tearing the halves into halves,
will you always have paper left?
What is the smallest unit
eventually left?
Atoms and Molecules
• Atom- smallest part of
an element that has
properties of that
element.
– All have same basic
makeup
– H2- 2 Hydrogen atoms
Atom
• Moleculecombination of 2 or
more atoms.
• Ie. O2, H2O, CO2
Building Block of Matter
• Element- substance that cannot be
broken down into any other
substance by chemical or physical
means. (simplest type of a pure
substance.)
• A substance consisting entirely of
atoms having identical chemical
properties.
• *All of the matter around you is
composed of one element or a
combination of two or more
elements.
Elements in the Body
• What elements do you think are the most
abundant?
• O,H, C and N
• What do you think a trace element is?
• Trace elements in the body are Selenium,
Mercury, Arsenic and Lead.
• All of the elements in the human body
could be bought for $118.63.
Atom structure
Electrons
electron
neutron
proton
• An atom consists of a
nucleus surround by
one or more electrons.
• The nucleus is made
up of protons and
neutrons.
• The electrons travel
around the outside.
Nucleus with p+
and neutrons
Chemical Symbols to Know
Oxygen- O
Aluminum- Al
Calcium- Ca
Hydrogen- H
Iron- Fe
Neon-Ne
Carbon- C
Sodium-Na
Phosphorus-P
Helium-He
Gold-Au
Potassium-K
Nitrogen- N
Silver-Ag
Iodine-I
Chlorine-Cl
Sulfur-S
Silicon-Si
Try these: How many atoms do
these molecules have?
• 2H20 = how many H? How many O?
• 3PO4 = how many P atoms? O atoms?
• 2C6H12O6 = C atoms? H atoms? O atoms?
Writing Chemical Equations
• Chemical Formulasshows the ratio of elements
in the compound.
– CO2
• Symbols- each element has
a one or two letter symbol.
C, Ca.
– The first letter is ALWAYS
capitalized and the second
lower case.
• Subscript- small
number written to the
right of a symbol that
shows the number of
atoms of an element in
a molecule.
H2O + 1/2 O2  H2O2
Photosynthesis vs. Cellular
Respiration
• Photosynthesis
Captures energy
Chloroplasts in
plants
• 6CO2 + 6H2O 
C6H12O6 + 6O2
• Cellular Respiration
Releases energy
Mitochondria
• C6H12O6 + 6O2 
6CO2 + 6H2O
What do you notice about these two equations?
1.3, 1.4, 1.9, 1.43
Rates of Chemical Reactions: 3 ways
to increase the rate of a reaction
Concentration- amount of material you have
in a certain volume.
Surface area- more material exposed, the
faster the reaction
Temperature- adding heat to speed up
movement of particles.
Other ways to control the rate of
reactions.
• Catalyst- material that
increases the rate of a
reaction by lowering
the activation energy.
– Enzymes- biological
catalyst
– Enzyme-substrate
reaction
• Inhibitor- material
used to decrease the
rate of a reaction by
raising the activation
energy.
Isotopes
• Some isotopes are
radioactive.
They are used for
determining ages of
fossils.
• They are also used in
medicine.
– to treat cancer or as tracers.
– PET scans
• Ie.
12C- non radioactive (6p+,
6 neutrons)
14 C- Radioactive (6 p+, 8
neutrons)
(protons and electrons stay
the same, the neutrons are
different. If you add the
p+ and neutrons you get
12 or 14.)
Energy Levels
• 5 levels : K: n=1, L: n=2, M: n=3, N: n=4,
O: n=5
• 2n2 tells the number of electrons you can
have in each level (orbitals)
• Valence e-, located in outer shell.
• Ideally, shell wants to be full. Most you can
have in an outer shell is 8.
• Electrons can move or jump to other levels.
Orbitals and Electron Capacity of the First Four Principle Energy
Levels
Principle
energy level
(n)
Type of
sublevel
Number of
orbitals per
type
Number of
orbitals per
level(n2)
Maximum
number of
electrons
(2n2)
2
2
s
p
1
3
4
8
3
s
p
d
1
3
5
9
18
4
s
p
d
f
1
3
5
7
16
32
Electron Configurations
• I will help you write the electron configuration for
Lithium and Nitrogen.
• 1st: find number of electrons
• 2nd: write out 1s, 2s, 2px, 2py, 2pz, 3s, etc.
• 3rd: Show where you put electrons, one at a time in each
orbital.
• 4th: Write the configuration.
• You try Magnesium
• Li: 1s22s1
• N: 1s22s22p3
• Mg: 1s22s22p63s2
Chemical Bonds
• Atoms with unfilled orbitals in their
outermost shell tend to be reactive with
other atoms.
Chemical Bonds
• Force that holds atoms
together.
– Covalent, ionic,
Van der Waals, H bonds
• Chemical reactions
occur when bonds are
formed or broken.
Bonding Link
Weaker Bonds
• Van der Waals- slight
attraction between
oppositely charges
regions of molecules.
• They can hold large
molecules together.
• Gecko’s feet
• Hydrogen bonds- an
atom of a molecules
interacts weakly with a
H atom already taking
part in a polar covalent
bond. Holds together
N bases on DNA.
Compounds
• Compound- substance
made of 2 or more
elements chemically
combined in a specific
ratio or proportion.
• CO2
Carbon 1: Oxygen 2
Ratio 1:2
• Organic Compoundany compound that
contains Carbon.
How are molecules different
from compounds?
Covalent Bonds
• Non-polar: atoms share electrons equally
• Polar: share atoms unequally making a
slight difference in charge between the two
poles of the bond.
Polar Molecules
• Sometimes covalent bonds do • Water molecule. NH3
not share electrons equally.
How do you know it’s
polar?
• Some atoms in the molecule
have a slightly negative charge
and others have a slightly
(-)
positive charge.
O
• Polar: hydrophilic
H
H
• Nonpolar: hydrophobic
(+)
• Water Link
.
(+)
Water’s Temperature-Stabilizing
Effects
• Water tends to stabilize temperature because
it can absorb considerable heat before its
temp changes.
• Evaporation- H bond break
• Freezing- H bonds resist breaking
Features of Water
• Cohesion
– Hydrogen Bonding
causes water
molecules to stick
together, producing
surface tension.
Adhesion- sticks to
something else.
• Water Expands when
it Freezes
– Ice Floats because
it is less dense than
the water.
Solutions
• Mixture- material
composed of two or more
elements or compounds
that are physically mixed
together but not
chemically combined.
• Salt and pepper, sugar and
sand, etc.
• Solution- well mixed
mixture. Where all
components are evenly
distributed. Give an
example.
Solvent vs. Solute
• Solvent- part of the
solution present in the
largest amount. It
dissolves other
substances.
• Ie. water
• Solute- smallest
amount present that is
dissolved by the
solvent.
• Ie. sugar
Suspensions
Mixtures of water and non-dissolved
materials. Can you give any examples?
Common suspensions include sand in water,
fine soot or dust in air, and droplets of oil in
air.
1.5 Most cells have a narrow range of temperature and acidity
that they can survive. If there are extreme changes in the
environment, they may alter the structure of the protein and
the cells function.
• Can you explain this?
• Can you give any
examples of this?
• What do you know
about pH?
pH
• Measure of H+ concentration in a solution.
The greater the H+ the lower the pH scale.
• Acids- releases H+
• Bases- release OH-
ACIDS
• An acid is a substance
that tastes sour, reacts
with metals and
carbonates, and turns
blue litmus paper red.
• You can eat some foods
that are acidic, but other
acids are not safe.
• When acids react with
metals they are corrosive.
• When they react with
compounds made of
carbonate, a gas forms.
• Litmus paper is an
indicator of pH to test
whether a substance is
basic or acidic.
BASES
• Base- substance that
tastes bitter, feels
slippery, and turns red
litmus paper blue.
• “Opposites of acids”.
• Bitter tastes- soaps,
detergents, shampoos,
tonic water.
• Slippery- soap. Some
bases can irritate your
skin.
• Bases- Blue
• Don’t react with metals or
carbonates. If it is not an
acid, then it is probably a
base.
pH Scale
•
•
•
•
0-14
1- most acidic (H+)
14 most basic (OH-)
7 in neutral
What are some things that
you know are acidic?
What are some things that
you are are basic?
Scales of 10. Ie. A pH of 4
would have 10 more H+
than a pH of 5.
Where do you think they
fall of the pH scale?
Animated pH scale
Salts
• Salt is any compound that dissolves easily
in water and releases ions other than H+ and
OH-.
• Ionic compound formed when an acid reacts
with a base.
• HCl + NaOH  NaCl + H2O
• Salts dissociate into useful ions in the body
(Na+ and Ca++).
Buffers
• Weak acids and weak
bases that react with
strong acids or bases
to prevent sharp,
sudden changes in pH.
Hemoglobin (carries oxygen)
• Control pH to
maintain homeostasis. maintains a stable pH in red
blood cells (RBC).
Bicarbonate is a body buffer.
Buffer control (equations go both
ways)
HA
+ H2O  A+
H3O+
Weak acid + water  conjugate base + hydronium
HA + NaOH  Na+A-
A-
+
HCl 
HA
+
+
H2O
Cl-
Homeostasis in your body
• Blood pH must be between 7.3-7.5
• If blood pH increases to 7.8,
– tetany may occur where skeletal muscles cannot be
released from contraction.
– Alkalosis can be lethal (blood pH rises and is not
reversable).
• If it falls to 7, the person could go into a coma
– Respiratory acidosis- too much CO2 forms too much
carbonic acid and pH drops.
Molecules of Life
Ch. 3
1.4 The work that takes place in the cell is carried out by the
different types of molecules it assembles: proteins, lipids,
carbohydrates, and nucleic acids.
1.6 Cells are made up primarily of a small number of
chemical elements
•
•
•
•
•
•
Carbon C
Hydrogen H
Nitrogen N
Oxygen O
Phosphorus P
Sulfur S
• Carbon can join to
other carbon atoms in
chains and rings to
form large complex
molecules.
Carbon’s bonding behavior
• Can form 4 covalent bonds.
• Functional groups are atoms or groups of
atoms covalently bonded to a C backbone,
giving distinctive properties to the
molecule.
Functional Groups
• Hydroxyl
• Methyl
• Carbonyl
Carboxyl
Amino
Phosphate
-OH
-CH3
- CO (Ketone- inside)
or CHO (aldehyde- end)
-COOH (non-ionized)
or COO- (ionized)
-NH2 (non-ionized)
or –NH3+ (ionized)
- PO4 or - P
Where found
Hydroxyl Alcohols (sugars, amino acids); water soluable
Repeatedly in simple sugars
Methyl
Fatty acid chains: insoluable
Carbonyl Sugars, a.a.; water soluable
(aldehyde- end of C backbone, Ketone- interior of
C backbone)
Carboxyl A. a., fatty acids; water soluable, acid
Amino
a.a., nucleotide bases; water soluable, base
Phosphate Nucleotids (ATP), DNA, RNA, proteins,
phospholipids; water soluable, acidic
Methane
• In methane seeps, methane bubbles upward
from ocean floor.
– Archaea use methane as energy source and
release CO2 and H2 .
– Bacteria around them use the H2 and made H2S
using sulfate in water.
Process
• High water pressure and low temperatures “freeze”
the bubbling methane into an icy methane hydrate.
• They are vast and could break apart to release
methane gas if temp. rises. I tis unstable and
explosive.
• Million of years ago a huge release of methane
might have occurred increasing CO2 levels,
lowering the O2 levels.
• Indirectly, methane could have been responsible for
mass extinctions of plants and animals. (Permian)
– 95% of marine species, 70% plants and animals on land.
Monomers vs. Polymers
• Monomers- 1 unit
• Polymers- many units
• The process of joining
monomers to make
polymers is
polymerization.
• Ex: Sugars make up
starch, Amino acids
make up proteins, fatty
acid chains make up
lipids.
Chemicals in Organisms
• Carbohydrates are a
group of chemicals
that include sugars,
starches and cellulose.
They store energy and
provide shape to
organism
Sugars CH2O
• Monosaccharides- single
sugars
– Glucose, fructose, galactose,
ribose, deoxyribose
• Disaccharides- double sugars
– Sucrose (table sugar- glucose +
fructose), lactose (milk sugarglucose + galactose)
• Polysaccharides- many sugars
– Glycogen (E storage in animals),
starch (E storage in plants),
cellulose (structure of plant cell
walls.)
This is in linear form.
Lipids- can’t dissolve in water
• A group of chemicals that
include fats, oils, waxes,
phospholipids, and
steroids.(Sterols)
• Fats and oils provide long-term
energy storage. Triglycerides (3)
• Waxes repel water. Fatty acid chains
attached to alcohols.
• Phospholipids form membranes of
cells and control what enters and
leaves.
• Steroids serve structural and control
functions in your body. Ie.
Cholesterol (also in cell
membranes), sex hormones
Fatty acid chain (lipid)
Do you see the hydocarbon chain?
1.10 Macromolecules, such as lipids, also contain
high energy bonds.
• Why would lipids need high energy bonds?
This is unsaturated fat,
oils.
What do you think
unsaturated would look
like?
Proteins
• Large, complex
molecules composed of
many smaller molecules
called amino acids.
• There are 20 amino
acids.
Enzymes are proteins
that help control
chemical reactions.
H
H-N-C-C=O
H R OH Carboxyl
group
Amino
group
Amino and carboxyl
groups form peptide
bonds between them
to form a protein.
Peptide
bond, H20 is
lost
Metabolic Reactions
• Condensation- 2 molecules form (water is
released)
– Peptide bond
Hydrolysis- water requiring cleavage reaction
Both need enzyme reaction at functional group.
Protein functions
Function
Example
Movement
Actin and myosin- contraction of
muscle fibers
Collagen for bones, tendons,
ligaments and cartilage.
Structure
Regulation
Transport
Enzymes- control chemical
reactions
Hemoglobin- RBC carries Oxygen
Nutrition
Casein- found in milk. Stores
amino acids for use by newborn
animals.
Defense
Antibodies- immune system
Structures of proteins
• 1o- chain linked together in definite sequence
• 2o- helical coil (alpha) or sheetlike array (beta) where
chain is formed by interaction of H bonds, joining
side groups of a.a.
• 3o- result of interactions of R group forming 3-D
shape. Globular proteins.
• 4o- complexing of 2 or more polypeptide chains.
Identify protein structures.
Enzymes-proteins that speed up
chemical rxn’s
Functional
Group Transfer
One molecule gives up functional group,
other accepts
Electron transfer One or more e- are stripped from one
molecule and given to another
Rearrangement
Juggling of internal bonds coverts one
type of organic compound into another
Condensation
2 molecule combine to form a larger one
covalently
Cleavage
Molecule splits into two smaller ones
Structure determines function
• Sometimes substituting one amino acid in place of another
can cause a disease. Ie. Sickle Cell Anemia
• Heme group. 4 polypeptides tightly packed is a globin.
Each globin ( 2 forms- alpha and beta) is folded into a
pocket that holds a heme group that is a large organic
molecule with an iron atom at its center. It is a oxygen
transporter. AKA: Hemoglobin. If valine is substituted for
glutamate the protein turns from polar to non-polar.
Hemoglobin now called HbS. Stick together in rod shaped
clumps- sickle cell.
• Sometimes a mutation can occur, changing amino acid
sequence, changing the structure and thus function of the
protein.
• Denaturing proteins with heat can change function as well.
(Why you don’t heat breast milk in the microwave?)
Sickle Cell Anemia
• What would be some problems with having
sickle cells?
• Clumping of cells- circulatory problems
• Spleen enlargement- immune system
problems.
Nucleic Acids
• Large, complex
molecules that contain
hereditary or genetic
information.
• DNAdeoxyribonucleic acid
• RNA- ribonucleic acid
DNA or RNA?
Nucleotides (monomers of nucleic
acids)
• Some are involved in
metabolism.
– cAMP
– ATP
• Nucleotide coenzymes
transport H atoms and
e-.
AMP
– NAD+ and FAD
(Cellular respiration)
ATP
• ATP (adenosine
• ADP (adenosine
triphosphate) is where
diphosphate)
energy is stored when it is
– How many phosphates
are there?
released form nutrients.
– What do you think will
• What does it look like?
– N base: adenine
– 5’ C sugar: Ribose
– 3 Phosphate (PO4) groups
happen when you add
another phosphate?
Forming and Breaking Down ATP
• Energy is stored in
bonds.
• When you break
bonds you release
energy and when you
make bonds you store
energy.
• ADP + Pi + Energy  ATP
– Are we storing or releasing
energy?
• ATP  ADP + Pi + Energy
– Storing or releasing energy?
Pi +
Energy
ADP
ATP
Pi + Energy
DNA vs. RNA
DNA
Double Stranded
Base Pairs (A-T, G-C)
Deoxyribose sugar
RNA
Single Stranded
Base Pairs (A-U, G-C)
Uracil is used instead
of Tymine
Ribose Sugar
1.9 Living and non-living things are composed of
compounds. These compounds contain bonds that hold
them together. ATP, the energy source in cells, is stored
in the bonds.
• ATP- Adenosine
TriPhosphate
• When the bonds break
energy is released.
• When bonds form,
energy is stored.
Can you explain this analogy?
Energy in the Cell
• Energy is the ability
to do work.
• Cells get energy from
food and break down
nutrients to get stored
energy in the bonds
between atoms.
Growth and Repair
• To grow and develop,
the cells of organisms
must make many new
carbohydrates,
proteins, and lipids.
• In order for your body
to repair itself,
chemical reactions are
needed to produce
new cells to replace
the damaged ones.
Reproduction
• During reproduction,
many chemical
reactions take place.
• Ultimately, DNA and
it’s chemical make up
are essential for
information to be
passed on.
Test your skills
• Go to the following link, click on your text
book. Go to chapter 2 and look at SciLinks
and take the Self-Test. Good luck .
• Ch. 2 Review