Biochemistry - the reactions of biomolecules can be described

by the methods of organic chemistry

The Chemistry of Life
THE EXPERIMENT OF FRIEDRICH WÖHLER IN 1828
Bio= life
Chemistry = how things interact
Biochemistry= the branch of science in which you study
the chemical and physical processes that occur in an
organism.

I. Basics of Chemistry Functional group: an atom or group of atoms that show

characteristic physical and chemical properties
A. The Atom
- Smallest particles of an element
- Made of a positive nucleus surrounded by a
cloud of negative particles called electrons.
- All elements are listed on the periodic table.

B. Molecules
- When two or more atoms join together, they
form a molecule.
- CHEMICAL BONDS: interactions between the
Levels of Structural Organization in the Human Body
electrons.
- COMPOUND: If a bond joins different elements,
the new substance

Basic Themes

All living things make use of the same types of

biomolecules, and all use energy. As a result, all
living things can be studied using the methods of
chemistry and physics

The fundamental similarity of cells of all types makes it

interesting to speculate on the origins of life
- both cells and the biomolecules of which they
are made must have arisen ultimately from very
simple molecules, such as H2O, CH4, CO2, NH3,
N2, and H2
ATP and the Reactions for its Formation
Biomolecules
Gases present in the atmosphere of the early earth
included NH3, H2S, CO, CO2, CH4, N2, H2, and H2O

Allows us to answer questions related to molecular Experiments have demonstrated that important
nature of life biomolecules, such as proteins and nucleic acids, could
have arisen under abiotic (nonliving) conditions from
Chemical Foundations of Biochemistry reactions of these simple compounds.

Organic chemistry: the study of the compounds of - in the earth’s oceans

Carbon - on the surface of clay particles
- the cellular apparatus of living organisms is
made up of carbon compounds Biomolecules (Cont’d)
- biomolecules are part of the subject matter of Living cells include very large molecules, such as
organic chemistry proteins, nucleic acids, polysaccharides, and lipids
 - these biomolecules are polymers (Greek: poly +
meros, many + parts)
- they are derived from monomers (Greek: mono
+ meros, single + part)
--amino acids → proteins
--nucleotides → nucleic acids
--monosaccharides → polysaccharides
--glycerol and 3 fatty acids → lipids
Proteins and Nucleic Acids play a role in life processes.
II. Water Chemistry
B. Water has many characteristics that make it vital to
our bodies.
5. cohesion & adhesion polarity allows water to
stick to itself (cohesion) and to any charged
material (adhesion). Water can glue materials
together.
III. Macromolecules
- Very large molecules that make most of the
structure of the body
- Made of smaller pieces called monomers that
can be assembled like legos to form a variety of
structures. A large chain of monomers is called a
polymer
B. Carbohydrates
1. Monomer: monosaccharide (sugar)
2. Polymer: polysaccharide (starch)
3. Structure: rings of carbon with oxygen and hydrogen
attached; CH2O
4. Uses: energy, plant structure
5. Examples: sucrose, cellulose
Informational Macromolecules
Directionality in Macromolecules
Enzymes: a class of proteins that display catalytic
activity.
- the catalytic effectiveness of a given enzyme
depends on its amino acid sequence
Genetic code: the relationship between the nucleotide
sequence in nucleic acids and the amino acid sequence
in proteins
- theories of the origin of life consider how such a
coding system might have arisen
Molecules to Cells: Biomolecules (Cont’d)
Which came first…the chicken or the egg?
- catalytic activity associated with proteins
- coding associated with nucleic acids
It has been discovered recently that certain types of
RNA have catalytic activity and are capable of catalyzing
their own further processing RNA is now considered by
many scientists to have been the original coding
material
- it still serves this function in some viruses
The “RNA World”
- The appearance of a form of RNA capable of
coding for its own replication was the pivotal
point in the origin of life
- This original RNA both encoded for and
catalyzed its own replication
- In time, this system evolved to encode for the
synthesis of protein catalysts
- Even later, DNA became the primary genetic
material, and RNA took on only an intermediary
role in the synthesis of proteins
Stages in the Evolution of Self-replicating RNA Molecules
- A key point in the development of living cells is
the formation of membranes that separate cells
from their environment
- Some theories of the origin of life focus on
proteins
- according to one model, proteinoids aggregated
to form microspheres
DOUBLE-ORIGIN THEORY: the development of a coding
system and the development of catalysis came about
separately
- a combination of the two later in time produced
life as we know it.
(proteins). Proteins later prove to be more efficient
catalysts and able to carry out a variety of tasks.
5 PROTEINS TAKE OVER▾ Proteins take on a wide range
of tasks within the cell. Protein- based catalysts, or
enzymes, gradually replace most ribozymes.

THE VITAL IMPORTANCE OF A CELL MEMBRANE IN THE 6 THE BIRTH OF DNA ▲ Other enzymes begin to make
ORIGIN OF LIFE DNA. Thanks to its superior stability, DNA takes on the
role of primary genetic molecule. RNA's main role is
Replication and Reproduction
now to act as a bridge between DNA and proteins.

7 BACTERIAL WORLD A Organisms resembling modern

bacteria adapt to living virtually everywhere on earth
and rule unopposed for billions of years, until some of
them begin to evolve into more complex organisms.

The Biggest Biological Distinction-Prokaryotes and

Eukaryotes

Prokaryote: Greek derivation meaning "before the

From Membrane-Coated RNA to Bacteria
Journey to the Modern Cell
After life got started, competition among life-forms
fueled the drive toward ever more complex organisms.
We may never know the exact details of early evolution,
but here is a plausible sequence of some of the major
events that led from the first protocell to DNA-based
cells such as bacteria.
1 EVOLUTION STARTS ▲ The first protocell is just a sac
of water and RNA and requires an external stimulus
(such as cycles of heat and cold) to reproduce. But it will
soon acquire new traits.
nucleus”
- single-celled organisms
- include bacteria and cyanobacteria
Eukaryote: Greek derivation meaning "true nucleus"
- contain a well-defined nucleus surrounded by a
nuclear membrane
- can be single celled, such as yeasts and
Paramecium, or multicellular, such as animals
and plants

2 RNA CATALYSTS ▼ Ribozymes-folded RNA mole- cules

analogous to protein-based enzymes arise and take on
such jobs as speeding up reproduction and
strengthening the protocell's membrane. Consequently,
protocells begin to reproduce on their own.

3 METABOLISM BEGINS ▲ Other ribozymes catalyze

metabolism-chains of chemical reactions that enable
protocells to tap into nutrients from the environment.

From Membrane-Coated RNA to Bacteria

4 PROTEINS APPEAR ▲

Complex systems of RNA catalysts begin to translate

strings of RNA letters (genes) into chains of amino acids
 - If the change in positive (free energy
increases), the reaction will not occur as written
unless energy is supplied from an external
source
Cells:
The Basic Units of Life

First to View Cells

- In 1665, Robert Hooke used a microscope to

- examine a thin slice of cork (dead plant cells)
What he saw looked like small boxes
- Hooke is responsible for naming cells
- Hooke called them “CELLS” because they looked
like the small rooms that monks lived in called
Cells

The Cell Theory

- All organisms are made of cells.

How Do We Classify Living Organisms Today?
- 5-kingdom system takes into account
differences between prokaryotes
eukaryotes
- Provides classification for eukaryotes that are
neither plants nor animals
- Kingdoms are: Monera, Protista, Fungi,
Plantae, and Anamilia
Five Kingdoms, Three Domains
- The cell is the basic unit of life in all living things.
- All cells come from existing cells.
Types of Cells
and
- All cells, whether they are prokaryotic or
eukaryotic, have some common features
PROKARYOTIC CELLS:
1. Have no membrane covered nucleus
2. Have no membrane - covered organelles
3. Have circular DNA
4. Are bacteria

EUKARYOTIC CELLS

1. Have a nucleus
2. Have a membrane -covered organelles
3. Have linear DNA
4. Are all other cells
Biochemical Energetics
ORGANELLES
- All cells require energy to functions
- Organelles are structures that enable the cell to
- Light from the sun is the ultimate source of
live, grow and reproduce.
energy for all life on earth
- Photosynthetic organisms use light energy to CELL MEMBRANE
drive the energy-requiring synthesis of
- Outer layer of cell
carbohydrates
- Allows nutrients into the cell and wastes outside
- Non-photosynthetic organisms consume these
of the cell
carbohydrates and use them as energy sources
- The energetics of a chemical reaction CYTOPLASM
- if the change in free energy is negative (free
energy decreases), the reaction is Spontaneous - Cytoplasm a jelly-like fluid contained in the cell
as written that holds the organelles.
-
NUCLEUS CHLOROPLASTS
- Found only in plant cells
- The control center of the cell - Contains chlorophyll (makes plants green)
- Contains the Cell’s DNA - Where photosynthesis takes place
NUCLEOPLASM
Found in Plant and Animal cells:
- The principal function of the nucleoplasm is to Nucleus, Golgi Complex, Mitochondrion, Lyosomes,
program as a suspension substance for the Endoplasmic, Reticulum, Cell Membrane, Ribosomes,
organelles inside the nucleus. It also helps to Vacuoles
maintain the shape and structure of the nucleus Found only in Plant Cells:
Chloroplasts, Cell Wall
and plays an important role in the
transportation of materials that are vital to cell
ORGANELLES- Organelles are structures that enable the
metabolism and function.
cell to live, grow and reproduce.
NUCLEAR ENVELOP
Water and pH
- The nuclear envelope separates the contents of
the Nucleus from the cytoplasm and provides The Chemistry of Life
the structural framework of the nucleus. The Water and Biochemistry
nuclear membranes, acting as barriers that
prevent the free passage of molecules between WHAT DOES LIFE REQUIRE?
the nucleus and the cytoplasm, maintain the all Earth organisms…
nucleus as a distinct biochemical compartment. - require liquid water
MITOCHONDRIA - have a common set of biological molecules
- Power center of cell - can maintain homeostasis
- Provides the energy the cell needs to move, - can evolve
divide, etc. BIOMEDICAL IMPORTANCE
RIBOSOMES - WATER – predominant component of living
- Site where proteins are made organisms
- Cell parts are made of proteins - 60 % water in the human body
- “Factories of the cell” - a universal solvent (organic or inorganic)
ENDOPLASMIC RETICULUM - reactant or product in many metabolic reactions
- Transportation system of cell The water molecule has tetrahedral geometry.
- Rough ER-ribosome's attached
- Smooth ER- no ribosome's
- “Roadways of the cell”

GOLGI COMPLEX
- Packaging house of cell
- Packages, processes, and ships out the stuff the THE CHEMISTRY OF WATER
cell makes
- “UPS of the cell” Molecule: two or more atoms held together by chemical
LYSOSOMES bonds
- Digests food particles and cell parts Example: Water
- “Garbage men” - Water molecule: two hydrogen atoms bonded
- Protects cell by digesting foreign invaders to one oxygen atom
- “Police men” WATER IS A POLAR MOLECULE
VACUOLE - Water is a "polar" molecule, because there is an
- Stores water, food & wastes uneven distribution of electron density. Water
- Vacuole is largest organelle in plant cell has a partial negative charge (∞ -) near the
CELL WALL oxygen atom due the unshared pairs of
- Found only in plant cells electrons, and partial positive charges (∞ +)
- Protects and supports the cell near the hydrogen atoms.
THE CHEMISTRY OF WATER HOW DO YOU MEASURE THE PH OF A SOLUTION?

The Properties of Water - The pH of a liquid or solution is often an

Water is a polar molecule: important piece of information in science.
- Oxygen side is slightly negative - Measuring pH use pH test paper, pH indicator
- Hydrogen side is slightly positive sticks, or a pH meter.
- Electronegativity = how strongly the
CLASSIFICATION
atoms pull electrons
- H+ ELEMENTS= ACID
When molecules have no charges, they - Produce hydrogen ions in solution
are nonpolar
- ELEMENT + OH = BASE
WATER IS POLAR
- PRODUCE HYDROXIDE IONS IN SOLUTION
- In each water molecule, the oxygen atom
attracts more than its "fair share" of electrons pH OF SOLUTIONS
- The oxygen end “acts” negative - A measure of the concentration of H+ ions in a
solution
- The hydrogen end “acts” positive
- The more H+ ions in a solution, the lower the pH
- cuses the water to be POLAR
- Fewer H+ ions in solution, the higher the pH
- However, Water is neutral (equal number of e-
- Scale from 0 to 14
and p+) --- Zero Net Charge Examples:
THE CHEMISTRY OF WATER STRONG ACIDS:
The Properties of Water Sulfuric acid (H2SO4)
Due to its polarity, Water is a good Solvent HYDROCHLORIC ACID (HCI)
- Solute: what is being dissolved
- Solution: the solute in the solvent STRONG BASES:
Water SOIUM HYDROXIDE (NaOH)
Water can dissolve salts and hydrophilic (water–loving) CALCIUM HYDROXIDE (Ca(OH)2)
molecules because it is polar.
Water can dissolve acids and bases. FUNCTIONAL GROUPS THAT ARE WEAK ACIDS HAVE
GREAT PHYSIOLOGIC SIGNIFICANCE
Acid + base 🡪 salt + water
HCl + NaOH 🡪 NaCl + H2O - Carboxyl groups, amino groups, and phosphate
ACID = a substance that donates H+ ions to esters are present in proteins and nucleic acids,
solution most coenzymes and intermediary metabolites
BASE = a substance that accepts H+ ions
- Dissociation of weak acids and bases
Nonpolar & Hydrophobic Molecules

- Nonpolar molecules, such as oil, do not contain Laboratory safety is of utmost importance to ensure the
charged atoms. well-being of everyone working in a chemical laboratory.
- These atoms are called hydrophobic (water– Here is a summary of the basic laboratory safety
hating). guidelines and precautions outlined in the provided
information:
The pH scale is a measure of the relative amounts of
acids and bases in a solution. Basic Laboratory Safety Guidelines:
pH greater than 7 = basic
- Familiarize yourself with experimental
Pure water pH = 7 = neutral procedures and safety precautions.
- Plan your work carefully to prevent accidents.
pH lower than 7 = acidic - Only perform approved experiments.
- Use recommended amounts of chemicals.
- Record all data and observations.
 - Wear a laboratory gown.
- Gloves, masks, and hairnets should be used
when appropriate.
- Avoid wearing jewelry.
- Always wear goggles and other safety garments.
- Avoid wearing contact lenses.
- Keep flammable liquids away from ignition
sources.
- Promptly wash off corrosive substances spilled
on the skin.
- Remove chemical-spilled clothes immediately.
- Perform experiments involving toxic or corrosive
reagents inside a fume hood.
- Dispose of liquid wastes in designated
containers, not down the sink.
- Know the location and use of emergency
equipment.
- In emergencies, the instructor should be the last
to leave the laboratory.
- Keep chemicals and equipment inside the
laboratory.
- No eating, drinking, or smoking in the
laboratory.
- Keep your working area clean and orderly.
- Keep materials away from the edges of the
laboratory bench.
- Turn off unused burners.
Housekeeping:
- Keep your workstation clutter-free.
- Clear aisles and push stools under tables.
- Clean chemical spills promptly and correctly.
- Never touch broken glass with bare hands.
- Handling Chemicals:
- Treat all chemicals as toxic; do not touch, taste,
or smell them without instruction.
- When testing for odors, waft vapors using your
hand.
- Know the hazards of chemicals and safety
precautions.
- Check reagent bottle labels before use.
- Cover reagent bottles and waste containers
when not in use.
- Use a fume hood for toxic gases.
- Add acid to water when diluting, not the other
way around.
- Use an aspirator, not your mouth, for pipette
suction.
- Wash hands thoroughly before leaving the
laboratory.
-
Heating Substances:
- Don't point heated test tubes at others.
- Never leave a lit burner unattended.
- Turn off burners when not in use.
- Don't look into containers while heating.
- Be cautious with hot objects.
- Avoid rapid temperature changes with
glassware.
- Don't heat flammable liquids over open flames.
Handling Glassware and Equipment:
- Inspect glassware and equipment for damage.
- Carry long glass tubing vertically.
- Pull plugs, not cords.
- Ensure dry hands when handling electrical
equipment.
Accidents and Injuries:
;c
- Handle chemical spills on skin and clothing with
running water.
- Wash cuts with water and apply pressure.
- For chemical splash in the eyes, use eyewash
fountain.
- Don't touch someone connected to a live
electrical circuit.
- In case of fire, follow safety procedures.
Safety Measures and Waste Management:
- Refer to Material Safety Data Sheets (MSDS) for
safety measures.
- Always wear safety goggles and a laboratory
gown.
- Handle glassware and weighing apparatus with
care.
- Avoid contact with mercury; use proper
disposal.
- Follow safety precautions with unknown liquids.
- Tie back long hair and avoid loose clothing.
- Be cautious when working with open flames.
- Avoid inhalation of reagents.
- Avoid skin contact with reagents.
- Use separate droppers for different solutions.
- Transfer small amounts of solutions to beakers
before using droppers.
- Use spatulas or paper for solid reagents.
- Wash hands thoroughly after every activity.
LABORATORY EQUIPMENT AND APPARATUS
1. Beaker: A container for mixing and storing 29. Tripod: A three-legged support stand.
liquids. 30. Forceps: Tweezers for handling small
2. Erlenmeyer Flask: A flask with a cone- objects.
shaped bottom used for mixing chemicals. 31. Hot Hand: Protective glove for handling hot
3. Analytical Balance: A precise scale for objects.
measuring mass. 32. Burette: A graduated tube for precise liquid
4. Graduated Cylinder: A tall container with measurement.
markings for measuring liquid volume. 33. Burette Clamp: A clamp for securing a
5. Droppers: Tubes for transferring small burette.
amounts of liquids. 34. Spot Plate: A plate with wells for holding
6. Test Tube: A small tube for holding and small samples.
heating liquids or substances. 35. Petri Dish: A shallow, lidded dish for
7. Test Tube Rack: A holder for organizing test culturing microorganisms.
tubes.
8. Test Tube Holder: A tool for holding test
tubes safely.
9. Test Tube Brush: A brush for cleaning test
tubes.
10. Pipette: A tool for precise liquid transfer.
11. Aspirator: A device for drawing liquids into
a pipette.
12. Stirring Rod: A rod for mixing substances.
13. Policeman: A tool for transferring solid
materials.
14. Watch Glass: A shallow dish used to cover
beakers or hold small samples.
15. Evaporating Dish: A dish for evaporating
liquids.
16. Crucible: A small, heat-resistant container
for high-temperature experiments.
17. Crucible Tong: Tongs for handling crucibles.
18. Water Bath: A container for heating
substances indirectly with water.
19. Spatula: A tool for scooping and transferring
solids.
20. Mortar and Pestle: Tools for grinding and
pulverizing substances.

21. Funnel: A cone-shaped tool for pouring

liquids into containers.
22. Thermometer: A device for measuring
temperature.
23. Iron Clamp: A clamp for holding glassware.
24. Iron Stand: A stand for supporting
equipment.
25. Iron Ring: A ring for holding glassware
above a flame.
26. Wire Gauze: A mesh for evenly distributing
heat.
27. Hot Plate: A flat surface for heating
substances.
28. Bunsen Burner: A gas burner for heating.