lecture biology

Saba malik
bS-3
StatiSticS
chemical baSiS
University of gujrat

Lecture 2
Chemical Basis of Life
Why study chemistry in an Anatomy and Physiology class?
- body functions depend on cellular functions
- cellular functions result from chemical changes
- biochemistry helps to explain physiological processes,
and develop new drugs and methods for treating
diseases
2-2

Fig. 2.1
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life

Structure of Matter
Matter – anything that takes up space and has weight;
composed of elements
Elements – composed of chemically identical atoms
• bulk elements – required by the body in large
amounts
• trace elements – required by the body in small
amounts
Atoms – smallest particle of an element
2-3

Table 2.1

Fig 2.3b

A lack of iodine in one’s diet can
cause swelling of the thyroid
gland resulting in a GOITER. The
condition is reversible if iodine
is taken. (Don’t worry, we iodize salt)
Iodine is used by thyroid cells to
make hormones (chemicals released by one
cell into the blood and bind to a receptor on another cell,
which is one way cells talk to each other).
Fig 2.3b

Element
Compound
vs
(Emergent Properties)

Elements – composed of the same types of atoms
Compounds – composed of two or more types of atoms

Element
Compound
Ex) a bar of pure gold, nitrogen gas (N2), oxygen gas (O2)
- Any substance composed of two or more elements
- Any substance composed of only ONE element
Ex) Na+
Cl-
(table salt), H2O, CO2

EMERGENT PROPERTIES (EP’s)
+ =
Pure sodium (element) Chlorine (Cl2) gas (element) Na+
Cl-
Table Salt (Compound)
Fig 2.2

What are atoms made of
and how are they organized?
(The Bohr Model)
Niels Bohr
Danish Physicist
1885-1962

Nucleus Organization:

Atomic Structure
Atoms - composed of
subatomic particles:
• protons – carry a
positive charge
• neutrons – carry no
electrical charge
• electrons – carry a
negative charge
Nucleus
• central part of atom
• composed of protons and
neutrons
• electrons move around the
nucleus 2-4

proton
neutron
electron
charge mass
+1
0
-1
1 amu (dalton)
1 amu (dalton)
1/1836th
an amu (dalton)
amu = atomic mass unit
1 amu or 1 dalton = 1.67 x 10-27
kg
Subatomic particles
(sub = below, below the atom level)

How are the electrons “held” to the nucleus? Why
do they not just shoot away?
Electrons are held to the nucleus by the
electromagnetic (EM) force since electrons are
negative and the nucleus is positive – opposite
charges attract / like charges repel.

How are the protons “held” together in the nucleus?
Why do they not break apart due to the EM force?
The strong force holds the nucleus together. The strong
force is only “felt” at extremely small distances, which is
why the electrons do not feel it. You would need to be on the
nucleus to feel it. For example, if gravity were like this, you
would only feel it on Earth, but if you jumped up a few feet,
you would no longer be pulled down by it...

Electron Organization:
Electrons are present in shells and move around the
nucleus at a speed of ~2200 km/s. They can only be in
these shells and nowhere else!!
The first shell (n=1) can hold up to 2 electrons. That
means it can have 0, 1 or 2 electrons in it at any time.
The second shell (n=2) can hold up to 8 electrons.
There are many more shells, but you only need to
know the first three for AP Bio.
n=1
n=2
The third shell (not shown, n=3) can also hold up to 8 electrons.

Which shell contains higher energy electrons, shell 1
(n=1) or shell 2 (n=2)? Explain.
Shell 2. The further from the nucleus the electron, the
further it can fall toward the nucleus and therefore it
has more energy (a greater ability to accelerate
matter) than shell 1 electrons.
n=1
n=2

Electrons can jump between shells (called a quantum leap)
In order to get an electron to “leap” from n=1 to n=2,
what is required?
n=1
n=2

Electrons can jump between shells (called s quantum leap)
n=1
n=2
n=3
The nucleus is charged and therefore is pulling on
the electron. It will take energy to pull the
electron away from the nucleus and move it
further away to shell 2. This is analogous to
picking up a bowling ball. Earth is pulling on the
bowling ball like the nucleus is pulling on the
electron. It takes energy to pick up a bowling ball.
Fig 2.7

Atomic Number and
Atomic Weight
Atomic Number
• number of protons in the
nucleus of one atom
• each element has a unique
atomic number
• equals the number of
electrons in the atom
Atomic Weight
• the number of protons
plus the number of
neutrons in one atom
• electrons do not
contribute to the weight of
the atom
2-5

The atomic mass (A)
Why do we not add the electrons mass?
Electrons are soooo small relative to
protons and neutrons (1/2000th
the
size) that we ignore them.
= protons + neutrons

The atomic charge
Compare number of protons to the
number of electrons.
Ex. If there are 10 protons (+10) and 7
electrons (-7) the overall charge is
+3

What happens if we
change the number of protons ?
You change the identity of the atom (becomes a different element)
as well as the mass.

What happens if we
change the number of neutrons?
You change the mass and perhaps the stability....

Isotopes
Isotopes
• atoms with the same atomic numbers but
with different atomic weights
• atoms with the same number of protons
and electrons but a different number of
neutrons
• oxygen often forms isotopes (O16
, O17
, O18
)
• unstable isotopes are radioactive; they
emit subatomic particles
2-6

Isotopes are atoms that have the same
elemental identity (same number of
protons/same properties), but
different number of neutrons.

Certain ratios of protons to neutrons are unstable resulting in
breakdown of the nucleus (nuclear radiation).
Ex. 6 protons and 6 neutrons in a nucleus (Carbon-12) is stable, but 6
protons and 8 neutrons (carbon-14) is unstable and will undergo
radioactive decay to become stable. C-14 is called a radioactive isotope.
stable stable unstable

Radioactive decay

Carbon-14 (radioactive) will decay to Nitrogen-14 (stable). Seven protons and 7
neutrons in a nucleus is stable. An electron is shot out during the decay
making it dangerous and useful.
Radioactive decay

Clinical Applications
Radioactive Isotopes Reveal Physiology
• can be detected in the body using a scintillation
counter
• injected into the body
• different types taken up by different organs
• can be used to destroy specific tissues
• commonly used
• iodine-131 for thyroid function
• thallium-201 for heart function
• gallium-67 and cobalt-60 for cancer
• others used to assess kidney functions, measure hormone
levels and bone density changes 2-31

What if we alter the
number of electrons
?
If you alter the electrons, you simply change the charge of the atom

Review:
4. How many protons, neutrons and electrons does the
above element contain?

Review:
5. Which of the following models is correct according to
the Bohr model of the atom?

Molecules and Compounds
Molecules – particle formed when two or more atoms
chemically combine
Compound – particle formed when two or more
atoms of different elements chemically combine
Molecular formulas – depict the elements present
and the number of each atom present in the molecule
H2 C6H12O6 H2O
2-7

Electrons
• found in regions of space called electron shells (energy shells)
• each shell can hold a limited number of electrons
• for atoms with atomic numbers of 18 or less, the following rules apply:
• the first shell can hold up to 2 electrons
• the second shell can hold up to 8 electrons
• the third shell can hold up to 8 electrons
• lower shells are filled
first• if the outermost shell is full, the atom is stable
2-8

Ions
Ion
• an atom that has gained or lost an electron(s)
• an electrically charged atom
• atoms form ions to become stable
Cation
• a positively charged
ion
• formed when an atom
loses an electron(s)
Anion
• a negatively charged ion
• formed when an atom gains an
electron(s)
2-9

AIM: How do atoms interact with each other?
When are atoms
most happy ?
When their valence shell is full.

To be “happy” (stable) the sodium
atom will need to either get 7
electrons or lose 1. Which is
easier?
The sodium will give away its
outer shell electron.

Chlorine needs one electron for
its outer shell to be full.

Ionic Bond
• an attraction between a cation and an anion
Ionic Bond
• formed when electrons are transferred from one atom
to another atom
2-10

Chlorine has a higher AFFINITY
for the electron and therefore
the electron will “fall” from
sodium to chlorine.

When the piece of elemental sodium (countless
numbers of sodium molecules) is placed in the
chlorine gas in the video, all those ridiculous
number of electrons jump to the countless
chlorines. This causes all the molecules to
move around violently (heat up) and electrons
to jump between shells (give off light).

ions
Cation vs Anion
Ionic bond
When sodium loses an electron it becomes
positively charged (a cation). When chlorine picks it
up it becomes negatively charged (a anion). Cations
and Anions are collectively called ions = fully
charged atoms/molecules.

ions
Cation vs Anion
Ionic bond
The sodium and chloride ions are now attracted to
each other and form an ionic bond.
ionic bond = bond between two oppositely charged ions

Salt crystals
Na+
Cl-
crystals are repeating arrays of Na+
and Cl-
held together by the electromagnetic force.

Salt
-general name given to ANY ionic compound (not
just sodium chloride (Na+
Cl-
) held together in a
lattice structure.
Na+
Cl-
K+
Cl-
Mg2+
Cl2
-
Mn2+
Cl2
-
Ca2+
CO3
2-

Covalent Bond
Formed when atoms share electrons
•Hydrogen atoms form single bonds
•Oxygen atoms form two bonds
•Nitrogen atoms form three bonds
•Carbon atoms form four bonds
H ― H
O = O
N ≡ N
O = C = O
2-11

http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55
How else can atoms fill their outer shells?

http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55
Single Covalent Bond
In this case, to be stable and fill their outer shells, unlike in an ionic bond,
the atoms will SHARE their electrons to form a covalent bond.
H-
H or H2

F-
F or F2

Double Covalent Bonds (double bond)
O=
C=
O or CO2

Draw :
CH4 or H2O

Structural Formula
Structural formulas show how atoms bond and are
arranged in various molecules
2-12

Polar Molecules
Polar Molecule
• molecule with a slightly negative end and a slightly positive
end
• results when electrons are not shared equally in covalent
bonds
• water is an important polar molecule
2-13

Hydrogen Bonds
Hydrogen Bond
• a weak attraction between the positive end of one polar
molecule and the negative end of another polar molecule
• formed between water molecules
• important for protein and nucleic acid structure
2-14

Chemical Reactions
Chemical reactions occur when chemical bonds form or
break among atoms, ions, or molecules
Reactants are substances being changed by the chemical
reaction
Products are substances formed at the end of the chemical
reaction
NaCl ’ Na+
+ Cl-
Reactant Products
2-15

Types of Chemical Reactions
Synthesis Reaction – chemical bonds are formed
A + B ’ AB
Decomposition Reaction – chemical bonds are broken
AB ’ A + B
Exchange Reaction – chemical bonds are broken and formed
AB + CD ’ AD + CB (NaCl+ AgNO3→ NaNO3+ AgCl)
Reversible Reaction – the products can change back to
the reactants
A + B  AB
2-16

ALL CHEMICAL REACTIONS
INVOLVE ENERGY
• WHEN BONDS
FORM,
ENERGY IS
STORED
• WHEN BONDS
BREAK,
ENERGY IS
RELEASED
ATP = energy carrier of a cell

Metabolism
• All the chemical reactions that take place in
the organism
• These reactions need to be balanced to keep
the organism alive
– The balance is called homeostasis

Acids, Bases, and Salts
Electrolytes – substances that release ions in
water
Acids – electrolytes that release hydrogen ions in water
HCl  H+
+ Cl-
Bases – substances that release ions that can combine with
hydrogen ions
NaOH  Na+
+ OH-
Salts – electrolytes formed by the reaction between an
acid and a base
NaCl  Na+
+ Cl-
HCl + NaOH  H2O + NaCl 2-17

Acid and Base Concentrations
pH scale - indicates the
concentration of hydrogen ions in
solution
Neutral – pH 7; indicates
equal concentrations of H+
and OH-
Acidic – pH less than 7;
indicates a greater
concentration of H+
Basic or alkaline – pH
greater than 7;
indicates a greater
concentration of OH-
2-18

pH scale
• Most chemical reactions in humans take
place between 6+8
– However, stomach acid is 2-3
– Enzymes are pH specific

2.2 Introduction to Chemistry
Blood - 7.5 (lethal if more acidic than 7
and more basic than 7.8)
Stomach acid - 2 -3
A change in pH --in your body results
in halting some enzyme functions

Acid rain --contains sulfuric acid and nitric
acid
Acid rain pH < 5.6
Acid rain washes away vital
minerals from soil, kills aquatic
organisms & strip nutrients from
plants

Organic Versus Inorganic
Organic molecules
• contain C and H
• usually larger than inorganic molecules
• dissolve in water and organic liquids
• carbohydrates, proteins, lipids, and nucleic
acids
Inorganic molecules
• generally do not contain C
• usually smaller than organic molecules
• usually dissolve in water or react with water
to release ions
• water, oxygen, carbon dioxide, and inorganic
salts 2-19

Inorganic Substances
Water
• most abundant compound in living material
• two-thirds of the weight of an adult human
• major component of all body fluids
• medium for most metabolic reactions
• important role in transporting chemicals in the body
• can absorb and transport heat
Oxygen (O2)
• used by organelles to release energy from nutrients
• necessary for survival 2-20

• Solutions --Water is known as
the universal solvent
• Chemical properties of water are
important b/c they allow it to form
solutions (Uniform mixtures)

• Solute --That which is being
dissolved (sugar)
• Solvent --That which does the
dissolving (water)

Ionic Compounds --dissolve
readily in water b/c
water is polar
Polar covalent compounds --
dissolve in water

Inorganic Substances
Carbon dioxide (CO2)
• waste product released during metabolic reactions
• must be removed from the body
Inorganic salts
• abundant in body fluids
• sources of necessary ions (Na+
, Cl-
, K+
, Ca2+
, etc.)
• play important roles in metabolic processes
2-21

ORGANIC COMPOUNDS
• COMPOUNDS THAT CONTAIN
CARBON, HYDROGEN AND OXYGEN
IN DEFINITE PROPORTIONS.
• USUALLY ASSOCIATED WITH LIVING
THINGS

Organic Substances
Carbohydrates
• provide energy to cells
• supply materials to build cell structures
• water-soluble
• contain C, H, and O
• ratio of H to O close to 2:1 (C6H12O6)
• monosaccharides – glucose, fructose
• disaccharides – sucrose, lactose
• polysaccharides – glycogen, cellulose
2-22

CARBOHYDRATES
• BUILDING BLOCKS = SIMPLE SUGARS
(MONOSACCHARIDES).
• MONOSACCHARIDES INCLUDE
– GLUCOSE
– FRUCTOSE ISOMERS
– GALACTOSE
ALL THREE HAVE THE SAME MOLECULAR
FORMULA, BUT DIFFERENT STRUCTURE:
C6H1206
THESE MOLECULES ARE THE MOST COMMON
SOURCE OF ENERGY FOR LIVING THINGS.

Organic Substances
Carbohydrates
2-23

CARBON
• Carbon is important biological element
because it can form four bonds with other
elements and long chains or rings
• Polymer – large molecule made up of many
smaller units like starch
• Monomer – unit that makes up polymer;
glucose is the monomer for starch

GLUCOSE
• Monomer of starch, glycogen, and cellulose

MORE COMPLEX CARBS
• DISACCHARIDES
– MADE UP OF TWO MONOSACCHARIDES
CHEMICALLY COMBINED.
– GLUCOSE + GLUCOSE = MALTOSE
– GLUCOSE + GALACTOSE = LACTOSE
• THIS IS MILK SUGAR
– GLUCOSE + FRUCTOSE = SUCROSE
• THIS IS TABLE SUGAR
• These molecules store energy for later use

2. 3 The Compounds of Life
• Glycogen - animals stored
energy made from
sugars (same
saccharides)
• Cellulose - simple sugars that
make structural
carbos in plants

THE MOST COMPLEX CARBS
• STARCH – MADE UP OF MANY GLUCOSE UNITS
COMBINED.
– PLANT LONG-TERM FOOD STORAGE
• GLYCOGEN – MADE OF MANY GLUCOSE UNITS
COMBINED
– ANIMAL STORAGE IN LIVER AND MUSCLES
• CELLULOSE – MADE OF MANY GLUCOSE UNITS
COMBINED.
– PLANT CELL WALLS; FIBER
• CHITIN – PROTECTIVE COVERINGS IN INSECTS
AND OTHER ARTHROPODS; ALSO IN FUNGUS
CELL WALLS

DEHYDRATION SYNTHESIS
• In order for two molecules to join together, each
molecule must break off atoms to provide a
bonding place.
• Most organic molecules do this by losing a
hydrogen atom from one molecule and a hydroxyl
group from the other.
• These two join to form water, and allow the
molecules to make a bond.

Dehydration Synthesis
disaccharide
C6H12O6 + C6H12O6  C12H22O11 + H2O

Hydrolysis
• In order to break down a large molecule to
make smaller molecules, a molecule of
water has to be added.
• This fills in the spots where the bond broke
– one molecule gets a hydrogen atom, the
other gets the hydroxyl group.

Hydrolysis
ADD WATER
POLYSACCHARIDE
MONOSACCHARIDES
TO A
AND
FORM
MANY

Dehydration Synthesis and Hydrolysis
store and release energy
• Dehydration synthesis stores energy by
forming bonds.
– As in the formation of polysaccharides from
monosacharides
• Hydrolysis releases energy by breaking
bonds.

Organic Substances
Lipids
• soluble in organic solvents
• fats (triglycerides)
• used primarily for energy
• contain C, H, and O but less O than carbohydrates (C57H110O6)
• building blocks are 1 glycerol and 3 fatty acids per molecule
• saturated and unsaturated
2-24

Lipids: fats, oils, waxes, phospholipids,
steroids
• Used for longer-term storage of energy
• Fats – in animals
• Oils – in plants
• Waxes – water repellent (In your ears, beeswax, coat
plant leaves), waterproof bird feathers.
• Steroids – in animal cell membranes and some
hormones.
• Phospholipids – make up parts of cell membranes

A common fat = Triglyceride
• Composed of one glycerol and three fatty
acids, joined together by dehydration
synthesis:
G
L
Y
C
E
R
O
L
3
F
A
T
T
Y
A
C
I
D
S

Saturated and unsaturated fats:
• Saturated fats have no C=C bonds within the fatty
acids
– These are considered unhealthy – they clog up the
coronary (heart) arteries.
– These are solid at room temperature.
– From animals.
• Unsaturated fats have at least one C=C bond in
one of its fatty acids
– These are considered healthier.
– Plant oils are usually unsaturated.
– Liquid at room temperature.

Organic Substances
Lipids
• phospholipids
• building blocks are 1 glycerol, 2 fatty acids, and 1 phosphate per
molecule
• hydrophilic and hydrophobic
• major component of cell membranes
2-25

Organic Substances
Lipids
• steroids
• connected rings of carbon
• component of cell membrane
• used to synthesize hormones
• cholesterol
2-26

Organic Substances
Proteins
• structural material
• energy source
• hormones
• receptors
• enzymes
• antibodies
• building blocks are amino acids
• amino acids held
together with
peptide bonds
2-27

• Proteins - make enzymes that
help control chemical
reactions (ex. Speed up
digestion, releasing
energy during cellular
respiration, building up
proteins

• Proteins - large, complex
molecules composed of many
smaller molecules called
amino acids (only 20 amino
acids make different combinations &
proteins)
–Amino acids are held together by
peptide bonds to form proteins

PROTEINS
• Important for movement, structure, regulation,
transport, nutrition, and defense.
• Composed of building blocks called amino acids
• Humans cannot make these from scratch – we
must eat foods with proteins, then use the amino
acids to make our own proteins.

Amino Acids
• There are 20 different aa’s
• They are combined in various numbers and orders to
produce a great number of different proteins.
• Each aa has an amino group, an acid group (carboxyl), and
a variable group (there are 20 different variable groups).
• Amino acids attach to each other by dehydration synthesis
forming a peptide bond between the amino group of one aa
and the acid group of the other aa.
• Change the number or arrangement of the aa’s and the
protein is changed.

Amino acids
Acid group
Amino group

Dipeptide – two aa’s joined by a peptide
bond.

Organic Substances
Proteins
Four Levels of Structure
2-28

Nucleic Acids
• Molecules of heredity.
• DNA – deoxyribonucleic acid
– makes up chromosomes (GENES)
– Contains the genetic code
• Determines the organism’s traits
• Contains the code for making proteins
Which control the cell’s activities
• RNA – ribonucleic acid
– Helps DNA make proteins

• Nucleic Acids - large, complex
molecules that contain
hereditary or genetic
info – two types
• monomer – nucleotide (made up
of nitrogen base, phosphate, and
sugar)

DNA - carries instruction that
control activities of cell
(blueprint)

Organic Substances
Nucleic Acids
2-30

Enzymes – Special Proteins
• Change the rate of chemical reactions
without being used up themselves
(biological catalyst).
• Can be used over and over.
• Action is very specific –
each enzyme will only
work on one particular substance (the
substrate).

HOW DOES AN ENZYME
WORK?
• LOCK AND KEY
MODEL
• INDUCED FIT
MODEL

2.4 Chemical Reactions and
Enzymes
*Type of protein
*Act as a catalyst, speeding up
chemical reactions
1. Substrate- substance being
changed by enzyme
2. Active site- region on enzyme
where substrate attaches (this is
the enzyme substrate complex)

2.4 Chemical Reactions and Enzymes
3. Substrate is altered (bond
weakened) so that bond is
broken
4. Products released and enzyme is
unchanged (only the substrate
changes)
5. Enzyme is free to bond with
another substrate

*Enzyme affected by high
temperature

2.4 Chemical Reactions and Enzymes
Chemical Reaction – creation of
new substances by breaking or
forming chem. bonds
Carbs broken for energy
All chemical reactions involve energy
(absorbed or released)

Chemical Reactions and Chemical Equilibrium
Biological Example:
Glycolysis is shown to the right. The
circled numbers are enzymes.
Which reactions are reversible?
Which reactions are irreversible?
Those catalyzed by enzymes 3, 4, 6, 7, 8, 9, 10, and 11
Those catalyzed by enzymes 1, 2, 5 and 12

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