- **Acids, Bases, and pH**:

- Acids and bases are important concepts in chemistry.

- pH is a measure of the acidity or alkalinity of a solution.
- The Henderson-Hasselbalch equation and buffers are related topics.

- **What are Acids and Bases?**:

- Acids are substances that release hydrogen ions (H+) in water.
- Bases are substances that release hydroxide ions (OH-) in water.
- Acids and bases can be classified as strong or weak based on their ionization.

- **What is pH?**:
- pH is a measure of the concentration of hydrogen ions in a solution.
- It is calculated using the negative logarithm of the hydrogen ion concentration.
- pH values range from 0 to 14, with 7 being neutral, values below 7 acidic, and values
above 7 alkaline.

- **Henderson-Hasselbalch equation**:
- The Henderson-Hasselbalch equation relates the pH of a solution to the ratio of its
acid and conjugate base concentrations.
- It is commonly used in calculations involving acid-base equilibria.

- **Buffers**:
- Buffers are solutions that resist changes in pH when small amounts of acid or base
are added.
- They consist of a weak acid and its conjugate base or a weak base and its conjugate
acid.
- Buffers play a crucial role in maintaining the pH stability of biological systems.
<< The text provides an overview of acids, bases, and pH. It explains the definitions of
acids and bases, the concept of pH and its calculation, the Henderson-Hasselbalch
equation, and the role of buffers in maintaining pH stability. These concepts are
fundamental in understanding acid-base chemistry. >>
The Cell
Biochemistry and the Organization of Cells

Multidisciplinary Nature of Biochemistry

Title: What is Biochemistry?
- Biochemistry is the study of the molecular basis of life
- It uses principles from many sciences like chemistry, biology, and physics to
understand life processes at a molecular level
- Examples of its applications:
- Understanding health and disease at a molecular level allows for more effective
medical treatments

Biomolecules
Title: Basic Biomolecules
- Cells share the same basic biomolecules despite their diversity
- Biomolecules provide energy for cellular processes
- Key Terms:
- Carbohydrates
- Lipids
- Proteins
- Nucleic Acids

Cell Diversity
Title: Cell Diversity and Similarities
- Despite their diversity, cells share fundamental properties
- All cells contain DNA and use the same basic biomolecules
- Key Terms:
- Eukaryotic cells
- Prokaryotic cells Cell Transport Analogy Notes

Title: Cell Transport System Analogy to Cars, Buses, Taxis

Description: The text draws an analogy between molecules within a cell and forms of
transportation to describe how substances move within and between cells.

- Cars, buses, taxis = molecules that facilitate movement of substances within a cell
- Routes = specific reactions that occur within a cell
- Routes operate simultaneously, just like many cars, buses, and taxis moving at once
on roads
- Some molecules/vehicles have specialized functions, others can perform multiple roles
- Reactions/routes found in all cell types, some only in specific cell types

Cell Component Variability Notes (

Title: Variability in Cellular Components Between Organism Complexity

- More complex cells in larger, more advanced organisms contain more structural
features than simpler cells
- As organisms increase in complexity, their cells become larger and more varied in
internal structures to perform more complex functions

Origin of Life Notes

Title: Theories on the Origin of Life

Levels of Structural Organization Notes

Title: Hierarchical Organization of Structures in the Human Body

- Atoms → molecules → macromolecules → organelles → cells → tissues →

organ systems → whole organism
- Smallest to largest levels of organization in the human body (and generally in living
things)
- At each increasing level, structures become larger and more complex with specialized
functions that depend on cooperation of lower level structures

Chemical Foundations of Biochemistry Notes (Page 8)

Title: Biochemistry Begins with Basic Chemistry

- All biological processes have a foundation and basis in basic chemistry

- Cells, tissues and living systems are ultimately made of atoms and molecules following
chemical rules and reactions
- Understanding chemistry is crucial for understanding the biochemical processes that
sustain life ORGANIC CHEMISTRY NOTES

The study of carbon compounds and their derivatives

- Organic chemistry is the study of compounds of carbon and hydrogen and their
derivatives
- Part of organic chemistry involves the study of biomolecules

CAN A CHEMIST MAKE THE MOLECULES OF LIFE IN A LABORATORY?

- In the early 19th century, there was a belief that compounds found in living
organisms could not be produced in the laboratory due to "vital forces"
- German chemist Friedrich Wöhler synthesized urea, a waste product found in
animals, from ammonium cyanate in 1828
- This was the first time an organic compound was synthesized in the lab, disproving the
idea of "vital forces"
- Wöhler synthesized urea by heating ammonium cyanate

- Friedrich Wöhler (German chemist who first synthesized an organic compound

in the lab)
- Urea (waste product synthesized by Wöhler from ammonium cyanate)
- Ammonium cyanate (compound used by Wöhler to synthesize urea)
- Vital forces (early 19th century belief that living organisms contained forces that
prevented synthesis of organic compounds in the lab)

ORGANIC VS INORGANIC COMPOUNDS

- Organic compounds contain carbon and are found in/associated with living organisms
- Inorganic compounds do not contain carbon or are not associated with living
organisms
- Wöhler's synthesis of urea showed that organic compounds could be synthesized in
the lab from inorganic precursors

BIOLOGICAL UREA CYCLE

- Urea is produced from ammonia in the liver

- Urea is transported via blood to the kidneys and excreted or to other tissues
- Muscle and intestinal tissues can break urea back down into ammonia and other
compounds like glutamine and alanine

ORGANIC CHEMISTRY REACTIONS

- The reactions of biomolecules can be described using the methods of organic

chemistry
- Organic chemistry involves classifying compounds by their functional groups
- The reactions of molecules are determined by the functional groups present

- Functional groups (atoms or groups that determine characteristic reactions of

organic compounds like carboxylic acids, alcohols, amines, etc.)
- Organic reactions (reactions of carbon compounds studied in organic chemistry
classified by functional groups) Functional Groups of Biochemical Importance (Page 13)
Title: Important Functional Groups

Description: The text lists important classes of organic compounds found in

biochemistry and their characteristic functional groups. Functional groups determine the
reactivity and properties of biomolecules.

- Alkenes - contain a carbon-carbon double bond (C=C)

- Alcohols - contain a hydroxyl group (-OH) bonded to carbon
- Ethers - contain an oxygen atom bonded to two carbon atoms (-O-)
- Amines - contain an amino group (-NH2) bonded to carbon
- Thiols - contain a sulfhydryl group (-SH) bonded to carbon
- Aldehydes - contain a carbonyl group (>C=O) bonded to carbon and hydrogen
- Ketones - contain a carbonyl group (>C=O) bonded to two carbon atoms
- Carboxylic acids - contain a carboxyl group (-C(=O)OH)
- Esters - contain an ester group (-C(=O)OR) where R is an alkyl group
- Amides - contain an amide group (-C(=O)NR2) where R is usually hydrogen or an alkyl
group
- Phosphoric acid esters - contain a phosphoric ester group (-O-P(=O)(OH))
- Phosphoric acid anhydrides - contain a phosphoric anhydride group (-O-P(=O)-O-)

Title: Evolution of the Universe

Description: The text outlines the major events in the evolution of the universe from the
Big Bang to the formation of galaxies and the solar system.

- Big Bang Theory - the primordial fireball expanded rapidly after the initial explosion
approximately 13.8 billion years ago
- Early universe was extremely hot, around 15 billion Kelvin
- Cooled over hundreds of millions of years allowing formation of first stars/galaxies
- Stars formed from hydrogen/helium gases approximately 300 million years after
Big Bang
- Galaxies started to form and take shape around 1 billion years
- Solar system formed approximately 4.6 billion years ago from cloud of dust and
gas

Biologically Important Elements

Title: Formation of Chemical Elements

Description: The heavier elements crucial for life were formed via nuclear reactions in
stars over billions of years.

- Hydrogen, helium, lithium formed in Big Bang

- Heavier elements like carbon, nitrogen, oxygen, and others formed via:
- Thermonuclear fusion processes in first generation stars
- Supernova explosions dispersing material
- Cosmic rays interacting outside stars over billions of years
- Elements essential to biochemistry include carbon, oxygen, nitrogen, phosphorus, and
sulfur (Page 15)

Early Earth Conditions (Page 16)

Title: Early Earth Atmosphere

Description: The early Earth had very different atmospheric conditions than today.

- Little to no oxygen, dominated by other gases like carbon dioxide, nitrogen, methane
- Frequent volcanic eruptions released gases like hydrogen sulfide, ammonia
- Violent thunderstorms resulted from greenhouse effect of thick atmosphere
- Simple organic molecules like hydrogen cyanide, formaldehyde, sugars could have
formed from interaction of gases and energy like lightning (Page 16) Biologically
Important Elements
(Page 17)

Elements important for life:

- Hydrogen (H), Carbon (C), Oxygen (O), Nitrogen (N), Phosphorus (P), Sulfur (S)

Early Earth Atmosphere:

- Consisted of gases like ammonia (NH3), methane (CH4), carbon dioxide (CO2),
hydrogen (H2), water vapor (H2O)

Carbon and Nitrogen Sources:

- Methane (CH4) was converted to carbon dioxide (CO2), providing a carbon source
- Ammonia (NH3) was converted to nitrogen gas (N2), providing a nitrogen source
important for protein formation

Miller-Urey Experiment

The Miller-Urey Experiment:

- Simulated conditions of the early Earth atmosphere
- Contained water, methane, ammonia, and hydrogen gases
- Exposed to electrical sparks simulating lightning
- Formed simple organic compounds like formaldehyde (HCHO) and hydrogen cyanide
(HCN)

Failed Nucleotides Synthesis

Previous failed attempts:
- Chemists unable to find natural route for nucleobases, phosphate, and ribose to
combine and form RNA nucleotides

Chemicals Present in Early Earth:

- Phosphate, sugar, oxygen, carbon, nitrogen, phosphorus, nucleobases

A New Route to Nucleotides

Key Intermediate:
- 2-Aminooxazole molecule contains part of sugar and nucleobase, further reactions
yield ribose-base block and then nucleotide
- "Wrong" combinations don't survive ultraviolet exposure, "right" nucleotides do

Monomers and Macromolecules

Macromolecule Formation:
- Monomers link to form polymers or macromolecules

Key Macromolecules:
- Amino acids polymerize to form proteins
- Nucleotides polymerize to form nucleic acids
- Sugar monomers polymerize to form polysaccharides

Directionality in Macromolecules
(Page 20)

DNA Structure:
- Sequence of nucleotides determines genetic code

Protein Structure:
- Sequence of amino acids determines properties

Polysaccharide Structure:
- Order of sugars rarely affects properties

Polymerization Reactions:
- Involve elimination of water between monomers