Transcript Unit 2 - Biochemistry Notes

The Chemistry of Life!
Why are we talking about
chemistry????
Well….., because everything you dofrom walking, to thinking, to
digesting your lunch- is a series of
chemical reactions! We have to
understand basic chemistry in order
to understand cell biology and
genetics.
So, let the fun begin!!!!!
Levels of Biological
Organization
Matter

Matter – anything that has weight and
takes up space.


Includes solids, liquids, and gases
All matter is composed of elements.

There are 112 known elements

Ex. Iron, copper, silver, aluminum, carbon,
hydrogen, oxygen
Matter and Living Organisms


Living organisms require about 20
elements.
Of these, oxygen, carbon, hydrogen
and nitrogen make up more than 95%
of the human body.
Elements and Atoms



Elements are composed of tiny particles
called atoms.
Atoms are the smallest complete units
of elements.
Atoms vary in size, weight, and the
ways they interact with each other.
Atomic Structure

Nucleus



Protons (+ charge)
Neutron (neutral)
Electron cloud

Electrons (- charge)
Atomic number

The number of
protons found in the
nucleus of an atom
Mass number

The total number of
protons and
neutrons in the
nucleus of an atom
 Everything is made of matter
 Matter is made of atoms
Hydrogen
1 proton
1 electron
Oxygen
8 protons
8 neutrons
8 electrons
Proton +
Neutron 0
Electron –
The World of Elements
Ions

Ion = atoms that gain or lose electrons
become electrically charged



A cation is a positively charged ion
An anion is a negatively charged ion
An ionic bond is an attraction between an
anion and a cation
Animation: Ionic Bonds
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
How are ions important to
living things?

Ion Gated channels


Ions are often needed to move things into
and out of cells
Nerve impulses

Sodium and potassium ions are needed in
order for neurons to send impulses from
your brain to all the parts of your body and
back
How are ions important to
living things?

Muscle contractions
Calcium Ions are needed in
order to contract muscles to move


Cellular respiration
Hydrogen Ions are needed in
Order to get usable cellular
energy from our food

Isotopes



All atoms of an element have the same
number of protons but may differ in number
of neutrons
Isotopes are two atoms of an element that
differ in number of neutrons
Radioactive isotopes decay
spontaneously, giving off particles and
energy
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Cummings

Some applications of radioactive isotopes in
biological research are:



Dating fossils
Tracing atoms through metabolic processes
Diagnosing medical disorders
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
How do Isotopes form?

Lets read to find out!
Chemical Bonds

A bond is formed
when electrons
from two atoms
interact with each
other and their
atoms become
joined.
Molecules and Compounds


Molecule – when two or more atoms bond.
CO2 , O2 , H2 and H2O are all molecules.
Compound – when different elements
combine. CO2 and H2O are molecules, but
they are also compounds because they are
molecules containing more than one
element.
Molecules and Compounds

Molecules

Compounds
The formation and function of molecules depend on
chemical bonding between atoms
• Atoms with incomplete valence
shells can share or transfer valence
electrons with certain other atoms
• These interactions usually result in
atoms staying close together, held
by attractions called chemical bonds
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
Ionic Bonds


Because oppositely
charged ions attract,
sodium and chlorine
atoms that have formed
ions may react to form an
ionic bond
Sodium ions (Na+) and
chloride ions (Cl-) form
the compound sodium
chloride or table salt


Compounds formed by ionic bonds are
called ionic compounds, or salts
Salts, such as sodium chloride (table salt),
are often found in nature as crystals
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
Fig. 2-15
Na
Cl–
+
Covalent Bonds


Atoms can bond by
sharing electrons
instead of exchanging
them
Atoms like to have their
outer shell filled. If it is
not, they can share
electrons with another
atom who needs an
electron
Covalent Bonds Cont.



A molecule consists of two or more atoms
held together by covalent bonds
A single covalent bond, or single bond, is
the sharing of one pair of valence electrons
A double covalent bond, or double bond,
is the sharing of two pairs of valence
electrons
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
Fig. 2-12a
Name and
Molecular
Formula
(a) Hydrogen
(H2)
Electrondistributio
n
Diagram
Lewis Dot
Structure
and
Structural
Formula
Spacefilling
Model
Fig. 2-12b
Name and
Molecular
Formula
(b) Oxygen (O2)
Electrondistributio
n
Diagram
Lewis Dot
Structure
and
Structural
Formula
Spacefilling
Model
Polar v. Nonpolar Molecules



In a nonpolar covalent bond, the
atoms share the electron equally
In a polar covalent bond, one atom is
more electronegative, and the atoms do
not share the electron equally
Unequal sharing of electrons causes a
partial positive or negative charge for
each atom or molecule
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Cummings
Fig. 2-12d
Name and
Molecular
Formula
(d) Methane
(CH4)
Electrondistributio
n
Diagram
Lewis Dot
Structure
and
Structural
Formula
Spacefilling
Model
Fig. 2-12c
Name and
Molecular
Formula
(c) Water (H2O)
Electrondistributio
n
Diagram
Lewis Dot
Structure
and
Structural
Formula
Spacefilling
Model
Hydrogen Bond

Weak electrical
attraction between a
hydrogen atom and
another atom
Hydrogen Bonds


A hydrogen bond forms when a
hydrogen atom covalently bonded to
one electronegative atom is also
attracted to another electronegative
atom
In living cells, the electronegative
partners are usually oxygen or
nitrogen atoms
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
Fig. 2-16

+
Water
(H2O)


+
Hydrogen
bond
Ammonia
(NH3)


+

+
+
Bond Strength



Most of the strongest bonds in
organisms are covalent bonds that
form a cell’s molecules
Weak chemical bonds, such as ionic
bonds and hydrogen bonds, are also
important
Weak chemical bonds reinforce shapes
of large molecules and help molecules
stick to each other
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
Fig. 2-13
Water is a Polar Molecule
–
O

H
+
H
H2
O

+
How does polarity influence
the way molecules interact?
Opposites Attract!!!
Positively charged atoms
Are attracted to negatively
Charged atoms
More About Water


Water is cohesive – it sticks together
 Because of hydrogen bonding
 Creates surface tension – forms droplets
 Allows insects and leaves to rest on the surface of
water
Water is adhesive – it sticks to other things
 Because of hydrogen bonding
 Capillary action
 Water travels up the stem of a plant
 Meniscus forms at surface in graduated cylinder
Chemical reactions make and break chemical
bonds



Chemical reactions are the making
and breaking of chemical bonds
The starting molecules of a chemical
reaction are called reactants
The final molecules of a chemical
reaction are called products
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
Fig. 2-UN2
2 H2
O2
Reactants
2 H2 O
Reaction
Products
Anabolic and catabolic

Anabolic – Reactions that build molecules


Absorbs Energy
Ex. Photosynthesis

6 CO2 + 6 H20 → C6H12O6 + 6 O2


glucose is build from CO2 and water
Catabolic – Reactions that break molecules


Releases energy
Ex. Cellular Respiration

C6H12O6 + H20 + 6 O2 -- ATP + CO2 + H20

Glucose is broken down to from CO2 and water
ATP



ATP = Adenosine triphosphate
ATP is the form of energy that cells use
Adenosine molecule with 3 phosphate
groups attached
Adenosine
P
P
P
ATP – Adenosine Triphosphate
Adenine
Phosphate groups
Ribose
ATP




The charged phosphate groups act like the
positive poles of two magnets, they repel
each other
Energy is contained in the bond that holds
the phosphate molecules to the adenosine
When a bond breaks, energy is released
resulting in ADP (adenosine diphosphate)
Refer to pg 229 fig 9.2
Carbon is essential to life!!



All living things are composed mostly of
carbon.
All life on Earth is carbon based.
There are four basic types of organic
(carbon based) molecules.




Carbohydrates
Lipids
Nucleic Acids
Proteins
Organic v. Inorganic Compounds



Organic Compounds – contain
both Carbon and Hydrogen
Ex. Glucose (C6H12O6)
Other characteristics



Can be complex molecules found in
chains (linear), rings (cyclic), or
chains with branches
Contains Functional groups like
alcohols (OH), amino group
(contains N), carboxyl group (C, O
and H)
Has covalent bonds between the
atoms


Inorganic
Compounds – any
molecule that does
not contain both
Carbon and
Hydrogen
Ex. NaCl, H2O, CO2,
O2
Carbohydrates



Provide energy for cells
Carbohydrates include
sugars and starches.
Sugars - Monosaccharides,
disaccharides,
polysaccharides
Lipids






Lipids are insoluble (do not dissolve) in
water.
Lipids are fats
Lipids store energy.
Building Blocks - Fatty acids, glycerol
Saturated Fat – solid at room temperature
Unsaturated Fat – Liquid at room
temperature
This is what fatty acids look like
Organic Substances…Lipids

Phospholipids – similar to fat
molecules, however contains only
two fatty acid chains. In the
position of the third is a portion
containing a phosphate group



“head” – phosphate portion
(water soluble, hydrophilic)
“tail” – fatty acid portion
(hydrophobic)
Important in cellular structures
Organic Substances … Lipids

Steroids –
complex molecules
that include four
connected carbon
rings

Examples:
Cholesterol,
estrogen,
progesterone,
testosterone…
Nucleic Acids



Nucleic Acids –
store information
Theycontain the
genetic instructions
for all living things.
Two types of nucleic
acids


RNA
DNA
Proteins







Proteins serve as:
Structural materials
Allow chemical reactions to
happen in cells (Enzymes)
Energy sources
Hormones
Receptors on
cell surfaces
Antibodies
Organic Substances…Proteins


Proteins always contain nitrogen
atoms and sometimes sulfur atoms
The building blocks of proteins are
molecules called amino acids


There are 20 different amino acids
The shape or conformation of a
protein determines its function
Functional Groups
functional groups are groups of
atoms or bonds within molecules that
are responsible for the characteristic
chemical reactions of those molecules.
 Examples:
Hydroxyl –OH
Carboxyl –COOH
Carbonyl =CO
Amino –NH2
Phosphate –OPO3 Sulfhydryl -SH

What the heck is pH??


pH is the measure of the acidity of a
substance.
Acids release hydrogen ions (H+) when
they are mixed with water. The pH
scale is a measure of how acidic a
substance is.
More on pH! 

The pH scale ranges
from 0-14. 7 is
neutral. Substances
with a pH below 7
are acidic (acids).
Substances with a
pH above 7 are
alkaline (bases).
Ionization of water & pH

Water ionizes


H+ splits off from H2O, leaving OH–
+
 if [H ] = [ OH], water is neutral
+
 if [H ] > [ OH], water is acidic
+
 if [H ] < [ OH], water is basic
pH scale
how acid or basic solution is
 1  7  14
H2O  H+ + OH–

pH and H+ and OH- Concentration
H+ Ion
Concentration
100
0
10–1
1
–2
2
Stomach acid, Lemon juice
10–3
3
Vinegar, cola, beer
10–4
4
Tomatoes
10–5
5
Black coffee, Rainwater
10–6
6
Urine, Saliva
10–7
7
Pure water, Blood
10–8
8
Seawater
10–9
9
Baking soda
10–10
10
Great Salt Lake
10–11
11
Household ammonia
10–12
12
Household bleach
13
Oven cleaner
14
Sodium hydroxide
pH
Scale
tenfold change 10
in H+ ions
pH1  pH2
10-1  10-2
10 times less
H+
pH8  pH7
10-8  10-7
10 times more H+
pH10  pH8
10-10  10-8
pH
Examples of Solutions
100 times more H+ 10–13
10–14
Hydrochloric acid
Acids and Bases Cont.
Buffers & cellular regulation
pH of cells must be kept ~7




pH affects shape of molecules
shape of molecules affect function
pH affects cellular function
9
8
Control pH by buffers

reservoir of


7
H+
donate H+ when
[H+] falls
absorb H+ when
[H+] rises
pH

6
5
4
Buffering
range
3
2
1
0
0
1
2
3
4
5
Amount of base added
Enzymes


Enzymes are important proteins
because they speed up chemical
reactions.
Without enzymes, the chemical
processes carried out by your cells
would happen too slowly to keep you
alive!
Enzymes


Your body requires enzymes to
digest food and to convert fats and
carbohydrates to energy.
Some examples of enzymes are
pepsin, lipase, and lactase.
Enzymes
Lactose intolerance is an example of the trouble
that can be caused by an enzyme deficiency.
People who are lactose intolerant lack the enzyme
lactase. Lactase breaks down the sugar lactose. If
a lactose intolerant person consumes dairy
products, they can feel really sick. Fortunately,
lactase supplements are available to allow lactoseintolerant people to safely consume dairy products.
More about enzymes!




Each enzyme has a specific chemical
reaction it speeds up.
Pepsin breaks down proteins and is
found in your digestive tract.
Lactase breaks down lactose (a sugar
found in milk).
Lipase breaks down lipids (fats).
The Enzyme-Substrate Complex


Substrates are the
reactant(s) upon which
the enzyme acts
Enzymes form a
complex with their
substrates called the
enzyme-substrate
complex (ES complex)
at the active site

When the ES complex
breaks up it releases
product
This link shows how enzymes
work

http://www.lpscience.fatcow.com
/jwanamaker/animations/Enzyme
%20activity.html
This link shows how enzymes
work under various conditions!
http://www.kscience.co.uk/animat
ions/anim_2.htm
Enzymes Are Picky About
Their Working Conditions!



As we saw in the animation, enzymes need
the correct temperature or pH in order to
work.
If the temperature is too cold, or too hot, the
enzymes may not work.
Generally, chemical reactions happen more
quickly in warmer temperatures. But too
much heat can destroy an enzyme.
Enzymes are Very Sensitive



Each enzyme has an optimal
temperature, pH, and ionic strength
Human enzymes are optimized to
work at body temperature (37OC)
Certain body enzymes are most
active at the pH of a given body
compartment:
 Pepsin’s optimum pH matches
that of the stomach (acidic)
 Trypsin’s optimum pH is basic,
like the upper intestine
What does heat do to an
enzyme?

View animation of how heat affects the
structure of a protein.
Remember, enzymes are proteins!!!

Frying eggs

Picky enzymes!


Some enzymes need acidic conditions in
which to work, like the enzymes in your
digestive tract.
If an enzyme doesn’t have the right
conditions, it cannot do its job!
What factors affect enzyme
function?



We will be conducting a laboratory
investigation in order to answer the
question above.
For help in getting started, go to the
link below
Liver lab