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Ch2: Chemical Components of Cells

BSC 300
Lecture 2
Tuesday, August 25

Subatomic parDcles
posiDvely charged nucleus composed
of protons (+) and neutrons (no charge)
Number of protons is invariant for a
given element and denes its atomic
number
Electrical charge of protons is equal
and opposite to that of electrons
surrounding the nucleus

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Subatomic parDcles
For electrically neutral atoms, the number of protons and
electrons is the same

Chemical reacDvity the ability to form bonds is determined
by the atomic number: which also denes the # of electrons
Number of neutrons can vary (isotopes). This contributes to
nuclear stability, but doesnt alter chemical reacDvity of atoms

Nuclear parDcles and atomic measures

Atomic weight and molecular weight
is the mass of atom or molecule relaDve
to a hydrogen atom = number of protons
plus the number of neutrons.

Measured in units of Daltons = mass of one H atom (1 proton)

1 gram of H atoms contains 6.022 x 1023 atoms: Avogadros
number
1 mole of a substance contains 6.022 x 1023 (atoms, molecules,
marbles, what ever)

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Atomic measures
Well oZen refer to the concentra2ons of
substances in solu2on so be familiar with
the concept of molar concentraDon (M)
Hydrogen: H = 1 proton = 1g/mol
1M = 1g/L

Glucose: C6H12O6= 180 protons and
neutrons = 180g/mol
1M = 180g/L

There are only a small number of biologically

relevant elements
~25 elements essenDal for life
4 major elements in organic
material (96% of organic
weight): Carbon, hydrogen,
oxygen and nitrogen

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There are only a small number of biologically

relevant elements
Other 4%: Calcium, sulfur, phosphorous and potassium are
criDcal for organic molecules
While trace elements make up the rest: several metals like
iron and sodium, as well as chlorine and iodine

The outermost electrons determine how atoms

interact
Atomic nuclei do not parDcipate in chemical reacDons
Electrons are rearranged to form chemical interacDons
Electrons occupy discrete energy levels aka energy shells
Electrons closest to the nucleus are acracted most strongly and are
the most Dghtly bound

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The outermost electrons determine how atoms

interact
Each shell can hold only a
specic number of electrons
A lled outer shell renders the
atom chemically inert
Atoms with unlled outer shell
are chemically reacDve and can
parDcipate in chemical bonds

The outermost electrons determine how atoms

interact
This outer most shell is referred
to as the valence shell and for
low atomic weight atoms, the
electrons in this shell are the
chemically reacDve electrons,
aka the valence electrons.

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Chemical bonds occur via the sharing or transfer

of electrons
Atoms without a lled valence shell react with other atoms to form
chemical bonds, achieving stability by reaching a full valence state.
Ionic bonds: electrons are donated from one atom to another. The
result is an ionic compound.
Covalent bonds: Electrons

are shared between two atoms.
The result is a molecule.

Covalent bonds form by the sharing of electrons

The valence shell of hydrogen can
hold only 2 electrons, therefore H can
form only one covalent bond

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Covalent bonds are characterized by parDcular

geometries
Common organic elements can form mulDple covalent bonds
Bond number generates specic geometric arrangements around the
central atom.
Ex., Carbon can form 4 single bonds
producing a tetrahedron.

There are dierent types of covalent bonds

Single bonds result from sharing a single pair
of electrons by two atoms allows rotaDon in
the molecule around such bonds
double and triple bonds share 2 or 3 electron
pairs are shorter and stronger bonds which
prevent rotaDon.
AlternaDng double bonds are common
in carbon chains. Electrons are actually
shared across the molecule (or a part)
and stabilize it.

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Polar and non-polar covalent bonds

In non-polar bonds electrons are shared equally, such as between
two carbon atoms, or in diatomic oxygen
In polar covalent bonds one atom has stronger anity
(electronegaDvity) for the shared electrons which are pulled
closer to that atom.
Such molecules are polar parDal posiDve
and negaDve charges are formed in the
pair of atoms due to this unequal sharing

Oxygen and nitrogen are highly

electronega2ve.

Covalent bonds are strong and vary in strength

Bond strength reects the energy required to break the bond
Usually measured in units of kilocalories (or kilojoules) / mol
1 kcal is the amount of energy needed to raise the temperature of one L
or water by 1C. = 4.2 kJ.

Covalent bond strength is on average about 100 Dmes greater than

the kineDc energy of molecules in cells, making them very stable
Therefore breaking bonds requires considerable cellular energy and
the funcDon of important biological catalysts called enzymes (CH 3)

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Ionic bonds: Gain and loss of electrons

Atoms that obtain a lled valence by the
gain or loss of a singe electron can form
ionic bonds
Sodium and chlorine for example
Loss of an electron produces an ion with a full posiDve charge: a
caDon. Gain of an electron full negaDve charge: an anion
Oppositely charged ions form salts via electrosta2c a6rac2on. But
ionic bonds are weak and disassociate in water, a polar molecule.
Many biologically important ions

Noncovalent bonds help bring molecules

together in cells
Though weak and transient, ionic bonds and other noncovalent
interacDons play important roles in forming large organic molecules
CollecDvely thousands of such acracDons help shape
and hold together large molecules

Even weaker than ionic bonds are electrostaDc

acracDons between parDally charged regions of
molecules that result from polar covalent bonds:
hydrogen bonds

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Hydrogen bonds
Polarity of water molecules provides electrostaDc acracDon between
oppositely charged regions. Each water molecule can form 4 H-bonds
one at each H and two at the O.
Extremely weak and can be broken by thermal moDon, but
collecDvely, thousands or millions are formed between molecules,
within molecules or between molecules and the water in which they
are dissolved.

Charge, polarity and dissolvability

Hydrophilic: Polar covalent molecules and ions readily dissolve in
water. H-bonds lead to aqueous shell forming around them.
Hydrophobic: Molecules without polarity, such as oils and fats, aka
hydrocarbons, contain only, or mostly, carbon and hydrogen. Have
no polarity in their bonds and therefore are not acracted to water.

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Some polar molecules form acids and bases in

water
In strong polar covalent bonds H has very weak hold on electron pair
In soluDon, the H nucleus (a proton) is acracted to water molecules;
it dissociates and joins water to form a hydronium ion (H30+)
Acids are substances that release protons when dissolved in water
Even occurs between water
molecules
ConcentraDon in pure water
10-7M

Some polar molecules form acids and bases in

water
By convenDon the concentraDon of H30+ is wricen as H+ and is
expressed in a logarithmic scale where pH= - log10[H+]
Strong vs. weak acids reects their tendency to give up protons
readily in soluDon

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Some polar molecules form acids and bases in

water
bases accept protons when dissolved in water and in doing so
increase the OH- concentraDon of the soluDon
H+ and OH- are highly reacDve. Can
modify chemistry and funcDon of
biological molecules by associaDon/
disassociaDon of H+.
Buers: Molecular agents within cells
that maintain a relaDvely neutral pH
(pH=7) funcDoning as both acids and
bases, Ex. carbonic acid hydrogen
carbonate:

Small molecules in cells

Organic molecules: compounds that contain carbon
Carbon can form large molecules due to:
4 unpaired electrons can form up to 4 covalent bonds
C-C bonds are highly stable can form long chains (straight or
branched) as well as rings

Several important chemical groups can be acached to these carbon

skeletons to form an endless variety of organic molecules with highly
specialized funcDons
Review panel 2-1 and be able to idenDfy (by composiDon or
descripDon): methyl, hydroxyl, carboxyl, carbonyl, phosphoryl and
amino groups

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Chemical groups

Chemical groups

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Cells contain 4 major families of small organic

molecules
These are in turn the building blocks for the 4 large macromolecules
Sugars, amino acids and nucleoDdes serve as monomers to build the
larger polymers (polysaccharides, proteins and nucleic acids)
Facy acids are subunits of (but not monomers) of fats and lipids

Sugars are both energy sources and subunits of

polysaccharides
Sugars and their polysaccharides are aka carbohydrates
sugar monomers have the formula (CH2O)n where n=3-6
All contain one carbonyl group
All other carbons: one hydroxyl group
Arrangement of these groups can
vary so that molecules with same
chemical formula have dierent
structure: isomers
This does li6le to alter their chemical
proper2es but aects the ability of
specic enzymes to recognize and
process them.

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Sugars are both energy sources and subunits of

polysaccharides
In aqueous soluDons sugars adopt a ring
structure

monosaccharides are linked to form

disaccharides
condensaDon reacDon: bond between OH
groups on two sugars releases a H2O
molecules forming a glycosidic linkage
The reverse reacDon breaks the glycosidic
linkage by consuming a molecule of water:
Hydrolysis
Large number of OH in sugar monomers
allows branching and the generaDon of
diverse polysaccharides
Energy storage/transport, structural support,
protein and lipid modicaDon

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monosaccharides are linked to form

disaccharides
In soluDon the OH on the anomeric
carbon alternates between up () and
down () posiDons
ResulDng glycosidic linkages are either
or

Karp, Cell and Molecular Biology, Fig 2-16

monosaccharides are linked to form

disaccharides
HydrolyDc enzymes are specic to one form or another
This is why we can digest storage polysaccharides like starch (with
linkages) , but not structural polysaccharides like cellulose (with
linkages).

Karp, Cell and Molecular Biology, Fig 2-17

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AddiDons to sugars modify their chemistry

Such modied sugars play a variety of
import roles including protein
modicaDon and prokaryoDc cell walls.

Facy acids and derivaDves are Lipids

Lipids are a diverse group of nonpolar molecules dened as facy
acids or their derivaDves and being insoluble in water but soluble in
organic solvents.
FAs are unbranched hydrocarbons with one carboxyl group; thus they are
amphipathic.
Saturated FAs lack C=C double bonds and are solid at room temperature.
Unsaturated FAs have one or more C=C double bonds and are liquid at
room temperature.

Soaps consist
of facy acids

Karp, Cell and Molecular Biology, Fig 2-20

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Facy acids and derivaDves are Lipids

FA tails vary in length and can be saturated or
unsaturated
UnsaturaDon (C=C double bonds) produces
kinked tails that inhibit packing

Facy acids as a source of energy

Triacylglycerols: Fat droplets are composed of 3 FA tails joined by
ester bonds to glycerol
About 6 Dmes as much energy, weight for weight, as glucose

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Steroids: another category of lipids

Hydrocarbon in a linked 4-ring structure diverse roles in cell
signaling and structure (especially the plasma membrane)

Phospholipids form membrane lipid bilayers

One FA of a triglyceride is replaced
by a negaDvely charged phosphate
group linked to polar funcDonal
groups (like choline in this example)
making them strongly amphipathic.
As a result they readily form a bilayer
in aqueous soluDon with the
hydrophobic FA tails facing one
another and the charged head group
interacDng with water on both
surfaces.

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Amino acids are the subunits of proteins

General structure of all amino acids:
a central alpha carbon covalently bound to a H, and amino group and a
carboxyl group
At neutral pH, the amino and carboxyl groups are ionized: ie, they are
dipolar ions
4th posiDon: unique side group that denes chemistry of the amino acid
Thousands of possible side groups, but only 20 encoded geneDcally and
used in protein construcDon

Amino acids are the subunits of proteins

Be able to nd the side chain and determine
which family the amino acid belongs to. You
will not be expected to recognize and know
names of all amino acids.
There are a few that bear special
consideraDon: hisDdine, proline, glycine and
cysteine

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Amino acids are the subunits of proteins

Though stereoisomers are
possible, all biological
systems use and synthesize
only the L isomer

Basic amino acids

5 amino acids form ions in soluDon and therefore carry charge
3 basic amino acids

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Two acidic amino acids

Uncharged polar
Five have polar side chains and can
therefore parDcipate in H-bonding

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Remainder are uncharged nonpolar

The pepDde bond

Covalent link between the carboxylic acid of one AA and the amino
group of another
Because of the direcDon of translaDon, the pepDde sequence is
always wricen and presented with the amino terminus (N-terminus)
toward the leZ and C-terminus toward the right.

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NucleoDdes are the subunits of DNA and RNA

Know the general structure of a nucleoDde

Contain a nitrogen containing ring compound a base
Bound to a 5 carbon sugar, ribose or deoxyribose
Which is bound to one or more phosphate groups
Nucleosides lack phosphate groups

Be able to disDnguish pyrimidine from purine

and know which bases/nucleoDdes fall into
these two families and which are used in RNA vs
DNA

Two types of pentoses are used

Know the dierence between ribose (RNA) and deoxyribose (DNA)

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NucleoDdes can act as short term energy carriers

As with the well known ATP,
but GTP as well
Can be combined with other
groups to form coenzymes
necessary to acDvate specic
enzymes
And serve as important
intracellular messenger
molecules

Nucleic acids are polymers of nucleoDdes

NucleoDdes are joined by
phosphodiester bonds between the
5 and 3 carbons of two monomers
By convenDon nucleic acid
sequences are read from the 5 to
the 3 direcDon

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Macromolecules in cells

Each macromolecule contains a specic

sequence of subunits
Nucleic acids, polysaccharides and
pepDdes/proteins result from
condensaDon reacDons between
monomeric subunits
Facilitated by cellular enzymes that
process these reacDons only in one
direcDon (for example, 5 3 nucleic
acids and C-term N-term in proteins).
Specic order of the polymer leads to
unique funcDon of the polymer
Huge diversity in sequences (especially for
nucleic acids and proteins)

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Noncovalent interacDons
Are principle forces behind the 3-dimensional shape (conformaDon)
of macromolecules: This includes ionic bonds, H-bonds, as well as
Van der Waals acracDons and hydrophobic interacDons
Such interacDons depend on specic linear sequence of the polymer

Noncovalent interacDons
Are principle forces behind the 3-dimensional shape (conformaDon)
of macromolecules: This includes ionic bonds, H-bonds, as well as
Van der Waals acracDons and hydrophobic interacDons
Such interacDons depend on specic linear sequence of the polymer

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Van der Waals acracDon

Electrons are not in xed posiDons, but rather occupy spaces of
probability
Random uxuaDons in electron posiDons create regions of charge
even in nonpolar bonds
CollecDvely, such electrostaDc forces can create signicant acracDon
between molecules with complementary shapes

Hyrdrophobic interacDons
Are not acracDve forces, but instead result from repulsion of
hydrophobic regions from the aqueous environment. Water forces
such groups together to minimize their interacDon with water.

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Non covalent interacDons

Can be disrupted by changes in pH or salinity, but in biological
systems many are formed and increase molecular binding

Such forces provide highly specic inter- and

intra-molecular interacDons

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