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Bits of Chapters 2-5

The chemistry of life


Why do biology majors need
to understand chemistry?
Because living cells are made up of
chemical elements, many of which are
undergoing controlled chemical reactions.

These are the


chemical elements
that living cells
(and organisms)
are composed of
The human body is
the example here

Deficiencies in one of those


elements may lead to disease

Now we start the theme of emergent properties


(properties not found in the previous level)

Atoms
Molecules
Macromolecules
Cellular structures
Cells

Each element is a certain kind of atom


unique to it
The parts of an atom:
Nucleus
Protons (+)
Neutrons (neutral)

Electrons (-)
In orbits (shells)
around the nucleus)
In a pure state, an
elements number of
protons (+) and
electrons (-) are equal
and cancel their charges

Different elements are composed of


atoms that differ in the number of
protons, neutrons and electrons

This gives elements different properties

Electrons are in shells


The simple view:
Electrons and protons are
usually equal in number
Max 2 e- in the first shell
Max 8 e- in all the others
Elements like to fill their outer
shell to 8 (or 2 for Hydrogen)
Elements join together to form
molecules

Electrons have potential energy


(the potential to do work)
Electrons have more
potential energy the
farther they are from the
nucleus (ie: in the outer
shells
They can move from one
shell to another in
response to energy (next
slide)

Elements join together to form molecules


by forming chemical bonds
Strong bonds
Covalent bonds
Ionic bonds

Weaker bonds
Hydrogen bonds

Others

Covalent bonds
Sharing of electrons
in the outer shells
Share 2 - single bond
Share 4 - double
bond
Some elements pull
the electrons more
to them
(Electronegativity)

Electronegativity is a measurement of how


strongly an element pulls electrons towards
itself
O pulls e- much more than H
Ie: O is much more
electronegative than H
C pulls e- only slightly more than
H
Ie: C is slightly more
electronegative than H

Uneven sharing
(not very) polar covalent

Uneven sharing
polar covalent
Even sharing non polar covalent

Water is a polar molecule because of


this uneven sharing of electrons

This gives water many important properties!


(Well talk about these in Chapter 3)

Ionic bonds result when electronegativity


is drastically different between elements
Stealing (and donation) of
electrons

The strongest of bonds

Hydrogen bonds are weaker


chemical bonds

The binding of different elements


together leads to different shapes of
molecules

Shape of molecules is very important


for living cells and organisms
Structure and function go hand in hand!

Chemical reactions make and break


bonds, making new products for the
cell

These reactions occur in water (the


environment of our cells) (Chapter 3)
H2O is a polar
molecule
So
It can form
hydrogen bonds

Hydrogen bonds allow water


to stick to
Itself (cohesion)
Other molecules
(adhesion)
H bonds also
allow water to
function as

The universal solvent


Salt
(NaCl)
in water

Hydration
shell

Lysozyme - a water soluble protein

Because cells live in aqueous


environments and cells are composed
mostly of water on the inside
water influences quite a bit both inside
and outside the cell
1) Shape and structure of large molecules
2) Osmolarity
3) pH

Shape and structure of large


molecules
(remember that shape helps determine function)

Hydrophilic
Hydrophobic

Proteins
imbedded
in a
membrane
(Ch 7 fig)

A biological membrane (Ch 5 fig)

Osmolarity (very quick here)


Chap 7
fig

Less solutes than


The cell

The same concentration


of solutes as the cell

More solutes than the


cell

More on osmolarity in Chapter 7!

pH

Water
dissociates and
forms an
equilibrium

Proton (H+)

pH
Acids increase?
H+
(acids may also
decrease OH-)

Bases increase?
OH (bases may also
decrease H+)

pH affects living cells and


organisms big time
pH affects the rate of chemical
reactions, and so
is tightly controlled in you

Besides H2O, we are mostly


made of carbon (C) (Chapter 4)
(Organic Chemistry)
Why carbon?
Can form 4 covalent bonds

This leads to

A tremendous diversity of
shapes of carbon compounds
This leads to a great diversity of function

Note shorthand notation:


used when only C and H
are at the juncture

Certain chemical groups play a


key role in that functionality
Functional groups

You should know these by sight and be able to identify them!


You will see them as components of biological molecules!

Living organisms use carbon as


the building block to make large
biological molecules (Chapter 5)
Monomers (Molecules)
H2O

Polymers (Macromolecules)

Living organisms are constantly


breaking down and building molecules
(Metabolism - the chemical reactions of the cell)
Breaking down (like breaking down
food)
Catabolism
Hydrolysis
reactions

Living organisms are constantly


breaking down and building molecules
(Metabolism - the chemical reactions of the cell)
Building (making
macromolecules)
Anabolism
Dehydration
reactions

There 4 basic macromolecules that are


built by living organisms
(I.) Carbohydrates
(II.) Proteins
(III.) Nucleic acids
(IV.) Lipids

Think of the food calories!

I. Carbohydrates
Polymers of sugars
Monosaccharide
(simple sugar)
Hydroxyl groups
and 1 carbonyl
Formula (CnH2nOn)
Aldose vs Ketose
Glucose (C6H12O6)
is an important
building block

Glucose can fold on


itself

and form a polymer with itself


Starch
Storage

Glycogen
Storage

Cellulose
Structural

Glucose monomers
Glucose monomers

An example of building a glucose


disaccharide polymer (a carbohydrate)
C12H22O11

C6H12O6 + C6H12O6
H2O

C12H24O12 - H2O = C12H22O11


Ie: Subtract 1 H2O for each bond
created in a polymer

II. Proteins
Amino acids (monomer) >>> Peptides
Peptides >>> Polypeptides
Polypeptides >>> Proteins
Functions of proteins

Structure (structural proteins)


Cellular communication
Catalyze chemical reactions (enzymes)
Other

Amino acids are the building


blocks of proteins
An carbon
Amino group
Base (proton [H+]
acceptor)

Carboxyl group
Acid (proton donor)

R group
Affect shape and
functionality

There are 20
different amino
acids
(with 20 different
R groups)

Peptide bonds link amino acids


together
A dehydration
synthesis!
Between 2
functional
groups
Carboxyl
Amino

The amino acids and their


characteristics determine the
protein structure
Primary
Secondary
Tertiary
Quaternary

Primary structure
Linear chain of amino acids

Secondary structure
Hydrogen bonds stabilize regions of chains
helix and pleated sheet

Tertiary structure
3-D shape stabilized by side chain interactions

Quaternary structure
Association of 2 or more polypeptides
(some proteins only)

4 identical
polypeptides

4 polypeptides
2 different polypeptides

This structure (or shape) determines


functionality of the protein

III. Nucleic acids


Nucleotides (monomer) >>>
Nucleic acids
Nucleic acids
DNA
RNA

Function
Store and transmit hereditary
information

Nucleotides are the


building blocks of nucleic acids
Pentose sugar (5 C)
Deoxyribose (DNA)
Ribose (RNA)

Phosphate group
Nitrogenous base
One of 4
1 difference between DNA and RNA

Phosphodiester bonds link


nucleotides together

Phophodiester bonds

What kind of a synthesis reaction created this bond?


. Hydrolysis
. Dehydration

DNA usually exists as a double helix


RNA is usually in a single strand

The flow of genetic information is


usually from DNA to RNA to protein

IV. Lipids
Not polymers
Diverse group of hydrophobic
molecules
a) Fats
b) Phospholipids
c) Steroids

a) Fats
Function in
storage (C and
NRG), insulation,
padding
Glycerol + 3 fatty
acids
Ester linkage via
a dehydration
synthesis (again!)

(a hydrocarbon chain with a carboxyl group)

Saturated
v.
Unsaturated fats

b) Phospholipids
Hydrophilic
head
Glycerol
Phosphate
Choline

2 Hydrophobic
tails
Fatty acid
chains

Phospholipids self-assemble into


bilayers in an aqueous environment
This is the base for biological membranes

Other macromolecules integrate into


that phospholipid bilayer based on
their hydrophilic/hydrophobic
characteristics

Chapter 6

c) Steroids
Cholesterol (a membrane component in animal
cells)

Hydrocarbon chain

Hydrocarbon rings

(Chap 7 fig)

Cholesterol is also a precursor to make

c) Steroids
Steroid hormones

Testosterone

Estrogen

Note the hydrocarbon rings

Emergent properties
Atoms
Weve done this!

Molecules
Macromolecules
Cellular structures
On to cells!

Cells