BIOLOGY

Dr. Axel Kowald

Axel.Kowald@biologie.hu-berlin.de
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 AGENDA

The chemistry of life

Water and life
Carbon as basis for life
Biological macromolecules

Chapters 1, 2, 3, 4, 5
BIOLOGY, THE STUDY OF LIFE

What is life?

1. Composed of Cells
2. Maintain Homeostasis
3. Metabolism (Energy Processing)
4. Growth
5. Adaptation to the Environment
6. Respond to Stimuli
7. Reproduction
SCIENCE

Observation, testable explanations (hypotheses), tests (experiment)

Hypothesis: a tentative answer to a well-framed question

Experiment: a scientific test carried out under controlled conditions

SCIENTIFIC PROGRESS
MODEL ORGANISMS

E. coli C. elegans Danio rerio (Zebrafish)

Drosophila melanogaster S. cerevisiae Mus musculus

 QUESTIONS

A controlled experiment is one that:

A. Proceeds slowly enough that a scientist can make careful records of the
results
B. Has a treatment and a control group
C. Is repeated many times to make sure the results are accurate
D. Keeps all variables constant

Which of the following is an example of a qualitative data?

A. The fish swam in a zigzag motion
B. The contents of the stomach are mixed every 20 seconds
C. The temperature decreased from 200C to 150C
D. The six pairs of robins hatched an average of three chicks each
ORGANISMS ARE COMPLEX
CHEMICAL SYSTEMS
Elements: consist of
atoms and cannot be
broken down to other
substance by chemical
reactions. E.g. Iron, gold,
carbon

Compounds: consist of
molecules, which are
made of two or more
different elements in a
fixed ratio. E.g. Water,
salt, sugar
 ATOMS AND SUBATOMIC PARTICLES

Identical mass

Atomic nucleus
 ATOMIC NUMBER, MASS NUMBER

For convenience mass is measured in units of Dalton (1/12 of 12C atom = ~1 proton mass)
ISOTOPES
Same number of protons, but different mass.
The atoms differ by their number of neutrons.
Isotopes have identical chemical properties.

~99% ~1% <1%

Radioactive isotopes:
Decay spontaneously giving off particles and energy.
They transform to other elements.
PERIODIC TABLE OF ELEMENTS
ELECTRONS

Their distance from the nucleus defines their potential energy.

They are arranged into electron shells (electron orbitals). Each electron shell
has its potential energy level and defined distance from the nucleus.
 ELECTRON CONFIGURATIONS

Valence shell:
The outermost shell, relevant in chemical reactions, valence electrons
ELECTRON ORBITALS
The 3D space where an electron
is found 90% of the time
Maximal 2 electrons/orbital
The reactivity of an atom arises
from the presence of unpaired
electrons in one or more
orbitals of its valence shell

Superimposed orbitals
TYPES OF CHEMICAL
BONDS

Atoms with incomplete valence shells can interact with other

atoms in such a way that each partner completes its valence
shell. The atoms either share or transfer valence electrons.

Covalent bond
Ionic Bond Primary, strong
Metallic bonds

Hydrogen bonds
Van der Waals
Secondary, weak
Dipol dipol
COVALENT BONDS

The sharing
of valence
electrons by
two atoms
POLARITY

Different elements attract electrons with different strength.

This characteristic is called electronegativity and leads to
polar molecules.
ELECTRONEGATIVITY

• Fluorine has the highest electronegativity, but is of no biological relevance.

• Oxygen is biologically very important and has a very high electronegativity.
• The greater the difference in electronegativity, the more polar is the resulting
molecule.
IONIC BONDS
If the electron attraction of two atoms is too different one partner
completely takes over the electron (in contrast to sharing),
forming an atom with positive charge (cation) and one with
negative charge (anion). These atoms then stick together through
a ionic bond.
HYDROGEN & VAN DER WAALS
BONDING

Hydrogen bonds: weak forces

exerted between hydrogen and
more electronegative atoms in other
molecules (e.g. O, N, F)

Van der Waals forces: even weaker

forces between molecules caused
by temporarily induced dipoles
(through unevenly distributed
electrons).
QUESTION

Which statement is true of all atoms that are anions?

a. The atom has more electrons than protons
b. The atom has more protons than electrons
c. The atom has an equal number of electrons and protons
d. The atom has more neutrons than protons
LIFE ON EARTH

Life began in water and evolved there for 3 billion years, before spreading to land.

Ca. 70% of the Earth’s surface is covered by water.

Water has the rare property that its solid form has a lower density than its liquid form
(ice floats on water).
THE WATER MOLECULE,
H2O

V shape
Oxygen: high
electronegativity,
makes the H2O
molecule polar,
uneven distribution of
charge.

Many H bonds hold

water molecules
together
WATER AND
TEMPERATURE
PHYSICAL PROPERTIES
Temperature: a measure of the average kinetic energy of water
molecules in a body of matter. Independent of volume

Thermal energy: the kinetic energy associated with the random

movement of atoms or molecules is called thermal energy.

Calorie (cal): old unit of energy. The amount of energy it takes to raise
the temperature of 1g of water by 10C

Joule (J): new unit of energy. 1 calorie ↔ 4.18 joule

Specific Heat: the amount of energy that must be absorbed or lost for
1g of substance to change its temperature by 10C

Heat of vaporization: the amount of energy that must be absorbed for

1g of substance at 250C to change from the liquid to the gaseous state.

The high specific heat and high heat of vaporization of water is also due
to the hydrogen bonds.
WHY IS THIS IMPORTANT?

Because of the high specific

heat of water relative to other
materials, water will change its
temperature less than other
liquids when it absorbs or loses
a given amount of heat (water
buffers temperature
fluctuations).

Organisms are made primarily

of water, which helps them to
efficiently buffer their own
temperature and to cool via
sweating.
WATER, THE SOLVENT OF LIFE

Water is an excellent solvent because of its polarity.

Polar and ionic substances are hydrophilic, which means “water loving”
while nonpolar substances like oil are called hydrophobic
ACIDS AND BASES

Occasionally, a hydrogen atom participating in a hydrogen bond

between two water molecules shifts from one molecule to the other.
This is called the dissociation of water.

In pure water at 250C this happens only very rarely, so that the
equilibrium concentration of H+ (H3O+) and OH- is only 10-7 M.
H+ and OH- are very reactive substances.
In pure water H+ and OH- exist in equal quantities. But if acids or bases
are added, this changes dramatically.
MOLARITY

2 H2 + O2 → 2 H2O

2 molecules H2 + 1 molecule O2 → 2 molecules H2O

4 dalton + 32 dalton → 36 dalton

1 dalton = 1.7*10-24 g (1/12 of 12C)

1 mol = 6.02*1023 molecules (Avogadro‘s number)

1.7*10-24 g * 6.02*1023 = 1 g

2 mol H2 + 1 mol O2 → 2 mol H2O

4g H2 + 32g O2 → 36g H2O

ACIDS

An acid is a substance that increases the H+ concentration of a solution.

Hydrochloric acid (strong acid)

Carbonic acid (weak acid)

BASES

1. Reduce the H+ concentration by accepting H+ ions

2. Dissociate to OH- ions

THE pH SCALE

In any aqueous solution at

250C, the product of the H+
and OH- concentrations is
constant at 10-14

If enough acid is added to a

solution to increase [H+] to
10-5 M, then [OH-] will decline
by 10-9 M (10-5 x10-9=10-14)
BUFFERS
Human blood has a pH of 7.35 – 7.45
Buffers are substances that minimize changes in pH by accepting or donating H+
Most buffers are formed by a weak acid and its corresponding base.
The carbonic acid buffer helps to stabilize the pH of blood.

If the H+ concentration in blood begins to fall (that is, if pH rises), the reaction proceeds to
the right and more carbonic acid dissociates, replenishing hydrogen ions. But when the H+
concentration in blood begins to rise (if pH drops), the reaction proceeds to the left, with
HCO3- (the base) removing the hydrogen ions from the solution and forming H2CO3.
QUESTION

Which of the following is a hydrophobic material?

a. Paper
b. Table salt
c. Wax
d. sugar
CARBON, THE BACKBONE OF
LIFE

Of all the chemical elements, carbon is unparalleled in its ability to

form molecules that are large, complex, and varied, making possible
the diversity of organisms that have evolved on Earth.

The overall percentages of the major elements of life (C, H, N, O, P, S)

are quite uniform from one organism to another, reflecting the
common evolutionary origin of all life…
CARBON, CHEMICAL
PROPERTIES

CH4

CO2
6 electrons,
4 valence electrons,
4 covalent bonds:
large complex
molecules

urea
ISOMERS
Stuctural isomers Cis-trans isomers Enantiomers

Differ in the covalent The carbons have Mirror images of

arrangement of their covalent bonds to the each other.
atoms same atoms, but these They differ due an
atoms differ in their asymmetric carbon
spatial arrangements (attached to 4 diff.
atoms or groups)

C5H12
QUESTIONS

Choose the term that correctly describes the realtionship between these two
sugar molecules:
a. Structural isomers
b. Cis-trans isomers
c. Enantiomers
d. Isotopes

Identify the asymmetric carbon in this molecule:

CHEMICAL GROUPS 1
CHEMICAL GROUPS 2
QUESTION

Which functional group is not present in this molecule?

a. Carboxyl
b. Sulfhydryl
c. Hydroxyl
d. Amino

Which of the molecules shown has an asymmetric C?

MACROMOLECULES

All that diversity arises

from only 4 main classes
of macromolecules…

1. Carbohydrates
2. Proteins
3. Lipids
4. Nucleic Acids

The molecular logic of life is simple but elegant: Small building blocks
common to all organisms form the basis of unique macromolecules
MACROMOLECULES ARE POLYMERS

Proteins, Nucleic Acids, Carbohydrates

Chain like molecules of many similar/identical building blocks linked by

covalent bonds = polymer

Synthesis Breakdown
Condensation, dehydration Hydrolysis
CARBOHYDRATES

Sugars and polymers built of sugars monomers

A major energy source in the body

Classes:
1. Monosaccharides
2. Disaccharides
3. Polysaccarides
MONOSACCHARIDES

• Sugars can have between 3-7 C atoms.

• General molecular formula:
(CH2O)n glucose: C6H12O6
• Multiple hydroxyl groups (-OH)
• Carbonyl group (CO) at the end or in
the middle => aldose or ketose
PENTOSES AND HEXOSES IN
AQUEOUS SOLUTIONS
Ring formation
ALPHA & BETA GLUCOSE
DISACCHARIDES

Made of two Monosaccharides, Glycosidic linkage, Condensation reaction

Lactose: glucose + galactose

STORAGE POLYSACCHARIDES
Plants: starch 1-4 glycosidic bonds
1-6 glycosidic bonds at the branch points
Polymer of α-glucose
Forms granules in plastids
(chloroplast)
Animals can break down
starch in the digestive tract
Potato and grains are major
sources
STORAGE POLYSACCHARIDES II
Animals: glycogen
Polymer of α-glucose
Extensively branched
Liver and muscle cells
Reserve last for a day
STRUCTURAL POLYSACCHARIDES

Cellulose
Major component of cell walls
The most abundant organic compound
on Earth
Monomers of β-glucose
STRUCTURAL POLYSACCHARIDES II

Chitin
Major component of cell walls of Fungi
Exoskeleton of arthropods (insects,
spiders, crustaceans)
Monomers of β-glucose (like cellulose) but
with a N-acetylglucosamine group
QUESTION

The enzyme amylase can break glycosidic linkages between glucose

monomers only if the monomers are in the alpha form. Which of the
following could amylase break down?
a. glycogen, starch, amylopectin
b. Glycogen, cellulose
c. Cellulose, chitin
d. Starch, chitin, cellulose
LIPIDS

This class of molecules doesn’t form polymers

Hydrophobic
Large hydrocarbon regions

Biologically most important lipids:

1. Fats
2. Phospholipids
3. Steroids

Waxes, oils, pigments

FATS

Glycerol + fatty acids (16-18C)

= triacylglycerol = triglyceride
Glycerol is an alcohol Condensation reaction
SATURATED VS UNSATURATED
FATS
Unsaturated
cis-double bonds
leading to kinks

Saturated
No double bonds
The C binds the
maximal number of H

Energy storage, adipose tissues

Cushion vital organs, subcutaneous fat provides protection and heat
PHOSPHOLIPIDS

Cell membranes, amphipatic

CELL MEMBRANES AND MICELLES
STEROIDS

cholesterol Cholesterol is a steroid that is part of the

cell membrane in animals.
It is also a precursor for several other
steroids, some of which are
sex-hormones
QUESTION

Which of the following is true of unsaturated fats?

a. They are more common in animals than in plants
b. They have double bonds in the carbon chains of their
fatty acids
c. They generally solidify at room temperature
d. They contain more hydrogen than do saturated fats
having the same number of carbon atoms
 PROTEINS

50% of dry mass of most cells

20 amino acids
Unbranched polymers,
connected by peptide bonds
=> Polypeptides

Important for:
catalysis,
defense,
storage,
transport,
communication,
movement and
structural support.
DIVERSE FUNCTIONS OF PROTEINS
 Side chain
AMINO ACIDS

Amino Carboxyl
group group
AMINO ACIDS II
POLYPEPTIDE CHAINS

• Covalent peptide bond formed

by condensation reaction
• The purple area is the peptide
backbone
• The chemical properties of a
protein are determined by its
side chains.
• A protein has one N-terminus
and one C-terminus, giving it a
„direction“.
PRIMARY STRUCTURE

• The primary structure of a

protein is simply its amino
acid sequence.
• Proteins fold into a 3D
structure that is necessary
for their function.
• The folding happens
spontaneously or with the
help of chaperons.
• The prediction of the 3D
structure is a difficult
problem keeping many
scientists busy.
 SECONDARY STRUCTURE

• Regions of the polypeptide

fold into α-helices or
β-pleated sheets
• This is caused by
interactions between
elements of the peptide
backbone
• Hydrogen bonds are
formed between oxygen
atoms and hydrogen atoms
of amino groups.
• These interactions are
weak, but numerous.
 TERTIARY STRUCTURE
• Controls the overall shape
of a polypeptide
• Caused by interactions of
side chains
• Based on hydrogen bonds,
Van der Waals forces and
disulfide bridges between
cysteins.
• Hydrophobic side chains
are located inside the
protein core.
QUATERNARY STRUCTURE
Some proteins obtain their final shape by
assembling multiple polypeptide chains.

Hemoglobin
(two α and two β subunits)
Collagen
(three identical polypeptides)
HEMOGLOBIN
QUESTION
Which structural level of a protein is the least affected by a
disruption in hydrogen bonding ?
a. Primary
b. Secondary
c. Tertiary
d. Quaternary
NUCLEIC ACIDS
• The amino acid sequence of
proteins is determined by
genes on the DNA
• DNA is a nucleic acid made
up of nucleotide monomers
• Information is copied from
DNA to mRNA, another type
of nucleic acid.
• Ribosomes (large protein
complexes) are then
translating the information
from nucleotide sequences
into amino acid sequences.
• All the information is stored
in the DNA, but proteins are
required to „realize“ it.
NUCLEOTIDES
 NUCLEOTIDE POLYMERS

• Condensation reaction
joins 2 nucleotides via a
phosphodiester bond.
• This results in a
sugar-phosphate
backbone with a 5‘ and a 3‘
end.
• Information in the DNA is
stored in the sequence of
A, T, G & C bases.
• Similar to the binary
information in computers
but with 4 possible
symbols instead of 2.
DNA STRUCTURE
• Two antiparallel polynucleotide strands
form a double helix
• The sugar-phosphate backbone is on the
outside and the bases in the middle.
• Adenine always pairs with Thymine and
Cytosine with Guanin held together via
H-bonds.
• The complementarity of the strands is
important for copying the genetic
material during cell division.
RNA STRUCTURE
• RNA molecules are normally
single stranded, but very flexible
and can form internal base
pairings.
• Guanine pairs with Cytosine and
Adenine with Uracil.
• In addition to mRNA there are
many types of small RNAs
(tRNA, rRNA, siRNA) that are
important.
• In contrast to DNA, RNA
molecules can possess
enzymatic activities (ribozymes).
• According to the RNA world
hypothesis, in early evolution,
RNA was the carrier of genetic
information before DNA took
over.
QUESTION

Enzymes that break down DNA catalyze the hydrolysis of the covalent bonds
that join nucleotides together. What would happen to DNA molecules treated
with these enzymes?
a. The two strands of the double helix would separate
b. The phosphodiester linkages would be broken
c. The pyrimidines would be separated from the deoxyribose sugars
d. All bases would be separated from the deoxyribose sugars
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