INTRODUCTION TO BIOCHEMISTRY  Theodore Schwann

Biochemistry - “all animals are made of cells”

- study of the structure, composition, and chemical reactions of substances  Rudolf Virchow
in living systems - “all cells came from pre-existing cells”
- bio (life) + chemistry (alchemy) - 1855, German Physician
- the science concerned with the chemical basis of life -His statement debunked "Theory of Spontaneous
- it is also the science concerned with the chemical constituents of living Generation”
cells and with the reactions and processes they undergo. 3. Walter Flemming
- it is the application of the principles and methods of chemistry to the field -Discovered chromosomes in 1875; MITOSIS was identified
of biology and physiology 4. Carl Neuberg
- encompasses large areas of: - German chemist, coined the word chemistry
 Cell Biology- the branch of biology dealing with the study of - “Father of Modern Biochemistry”
cells, especially their formation, structure, components, and - beer fermentation
function 5. Hans Kreb
 Molecular Biology- the branch of biology that deals with the - proposed the Kreb cycle of the TCA in 1937; proponent of cellular
structure and function of the macromolecules (e.g., proteins respiration
and nucleic acids) essential to life 6. Embden and Meyerhof
 Molecular Genetics- branch of genetics that deal with the - Described the glycolytic pathway in 1925
structure and function of genes at a molecular level. 7. James Watson and Francis Crick
Supplement. - Described the double helical structure of DNA in 1953
8. Edward and Hans Buchner
Three areas of study in Biochemistry -Found that extracts from yeast could bring about
1. Conformational fermentation of sugar into ethanol in 1957
- the structure of conformation of biological molecules-DNA, RNA and 9. Paul Boyer and John Walker
protein transfer of information -Discovered the “rotary engine” that generated ATP in
2. Metabolism 1997
- energy production and utilization- Metabolism and the metabolic aspects 10. Jens Christian Skou
of cellular communication -Studied the “pump” that drives sodium and potassium across
3. Informational membranes
- language for communication inside and between the cells 11. Stanley Prusiner
-Discovered the organism that cause the BOVINE
Importance of Biochemistry SPONGIFORM ENCEPHALOPATHY “mad cow disease”
 In Physiology- Biochemistry helps one understand the 12. Ernst Ruska
biochemical changes and related physiological changes alteration in -Discovered the electron microscope and provided a whole new
the body, Pathology of any disease is studied through biochemical level of insight into cellular structure
changes
 In Pathology- based on the symptoms by the patient, the THE CELL
physician can get clue on the biochemical changes and the associated Cells
disorder/s - Smallest living unit; most are microscopic
 In Hormonal Deficiency- The formation, role of hormones in the Robert Hooke (1665)
normal body function is taught in biochemistry by which the -observed sliver of cork and saw “row of empty boxes”
physician can understand the concerned problem during the -coined the term “cell”
treatment -Pioneer in the study of CYTOLOGY
 In Nutrition Deficiency- In the present scenario, many people Robert Brown (1833)
rely in taking multivitamin and minerals for better health. The –discovered the nucleus
function and the role of vitamin in the body is described by Spontaneous Generation/ Abiogenesis
biochemistry - from a meaning ‘not’ + bios meaning ‘life’ + genesis
 In the field of Nursing- allowing nurses to determine how much meaning “beginning”
medicine should be prescribed or given to each patient they - the belief that living organisms were produced/ generated
encounter. Knowing the chemical components and reactions of drugs from nonliving sources. Example: frogs came from mud,
to human body and mixing the said drugs mice from sweaty clothing and flies from decaying meat
Principles of Cell Theory:
BIOCHEMISTS OF THE CENTURY  All living things are made of cells
1. Carl Scheele  Smallest living unit of structure and function of all organisms is
- Swedish founder of Biochemistry. He studied the the cell. They are the basic units of life.
chemical composition of matter in mid1700  All cells arise from preexisting cells (this principle discarded the
- He discovered Oxygen idea of spontaneous generation/abiogenesis)
2. Schleiden, Schwann and Virchow Chemicals of Life:
- formulated the cell theory in 1840  The most abundant chemical in cells is water.
 Matthias Schleiden  Other chemicals are called carbohydrates, and these are the
- “all plants are made of cells” energy source for the cell.
  Two other chemicals are proteins and lipids which are the
building materials for cells, much like wood and bricks are the
building materials of houses.
 Finally, nucleic acids are the genetic material.

 Organisms can be composed of only one cell or many cells.

 Unicellular or single celled organisms include bacteria the most
numerous organisms on Earth.
 Multi-cellular organisms are composed of many cells.
Cell Diversity
Cells within the same organism show Enormous Diversity in:  Size
 Shape  Internal Organization
a. Cell Size
 Cells are made of molecules
 Molecules are tiny particles of matter made up of atoms.
 The atom is the basic fundamental unit of matter.
 Atoms are made up of protons, neutrons and electrons.
 Female Egg - largest cell in the human body; seen without
the aid of a microscope
 Most cells are visible only with a microscope.
 Cells are small for 2 Reasons
Reason 1: Limited in size by the ratio between their outer
surface area and their volume. A small cell has more surface area than a
large cell for a given volume of cytoplasm.
Reason 2: The cell's nucleus (the brain) can only control a
certain amount of living, active cytoplasm.
b. Cell Shape
 Diversity of form reflects a diversity of function
 The shape of a cell depends on its function
c. Internal Organization
 Cells, the basic unit of life, are of 2 types: prokaryotic cells
(bacteria) and eukaryotic cells (fungi, algae, protozoa, plants,
and animals).

Organelles
-Very small (Microscopic); perform various functions for a cell
-Found in the cytoplasm; may or may not be membrane bound

3 Main Regions of the Cell/Cellular Organelles:

A. The Plasma membrane
-The boundary of the cell; Composed of three distinct layers:
1. Prokaryotes – The first Cells Two layers of fat and one layer of protein
-Cells that lack a nucleus or membrane bound organelles; - Composed of double layer of phospholipids and proteins
includes bacteria; Simplest type of cell; Single, circular - Surrounds outside of ALL cells; Controls what enters or leaves
chromosome the cell
- No membrane bound nucleus - Living layer; Molecules in cell membranes are constantly
- Nucleoid = region of DNA concentration moving and changing
2. Eukaryotes  Phospholipids
-Cells that HAVE a nucleus and membrane bound organelles; -Heads contain glycerol & phosphate and are hydrophilic (attract
Includes protists, fungi, plants, and animals; More complex water)
type of cells -Tails are made of fatty acids and are hydrophobic (repel water)
-Make up a bilayer where tails point inward toward each other
-Can move laterally to allow small molecules (O2, CO2, & H2O
to enter)
  Cell Membrane Proteins -Network of hollow membrane tubules
-Proteins help move large molecules or aid in cell recognition -Connects to nuclear envelope & cell membrane
 Peripheral proteins are attached on the surface (inner or outer) -Functions in Synthesis of cell products & Transport
 Integral proteins are embedded completely through the Rough Endoplasmic Reticulum (Rough ER)
membrane -Has ribosomes on its surface
o Cell Membrane in Plants -Makes membrane proteins and proteins for export
•Lies immediately against the cell wall in plant cells out of cell
• Pushes out against the cell wall to maintain cell -Proteins are made by ribosomes on ER surface. They
shape are then threaded into the interior of the Rough ER
 Cell Wall to be modified and transported
- Found outside of the cell membrane; Nonliving layer Smooth ER
- Supports and protects cell -Makes membrane lipids (steroids)
- Found in plants, fungi, & bacteria -Regulates calcium (muscle cells)
- Extra structure surrounding its plasma membrane in plants, -Destroys toxic substances (Liver)
algae, fungi, and bacteria.  Ribosomes
 Cellulose – Plants -Made of PROTEINS and rRNA
 Chitin – Fungi - “Protein factories” for cell
 Peptidoglycan – Bacteria -Join amino acids to make proteins through protein
B. Nucleus- The Control Organelle synthesis
-Controls the normal activities of the cell; Brain of Cell -can be attached to Rough ER or be free (unattached)
-Contains the DNA in chromosomes in the cytoplasm
-Bounded by a nuclear envelope (membrane) with pores  Golgi Apparatus
-Usually the largest organelle -A series of flattened sacs that modifies, packages, stores, and
-Each cell has fixed number of chromosomes that carry transports materials out of the cell.
genes; Genes control cell characteristics -Works with the ribosomes and Endoplasmic Reticulum.
-Contains thin fibers of DNA and protein called Chromatin. -Have a shipping side (cis face) & a receiving side
-Contains a small round nucleolus that produces ribosomal (trans face)
RNA which makes ribosomes. -Receive proteins made by ER
 Nuclear Envelope -Transport vesicles with modified proteins pinch off the ends
-Double membrane surrounding nucleus Materials are transported from Rough ER to Golgi to the cell
-Also called nuclear membrane membrane by VESICLES
-Contains nuclear pores for materials to enter & leave nucleus  Lysosomes -Recycling Center
 The Nucleolus (plural form: nucleoli) -Recycle cellular debris
-Inside nucleus -Membrane bound organelle containing a variety of enzymes
-Disappears when cell divides -internal pH is 5
-Makes ribosomes that make proteins -Contain digestive enzymes; Break down food, bacteria, and
 Chromatin worn out cell parts for cells
- DNA is spread out and appears as CHROMATIN in non- -Programmed for cell death (APOPTOSIS)
dividing cells; DNA is condensed & wrapped around proteins -Cells take in food by phagocytosis; Lysosomes digest the food
forming as CHROMOSOMES in dividing cell & get rid of wastes
C. Cytoplasm of a Cell
-Jelly-like substance enclosed by cell membrane Additional:
-Provides a medium for chemical reactions to take place  Cilia & Flagella
-Contains organelles to carry out specific jobs -Function in moving cells, in moving fluids, or in small particles
 Cytoskeleton across the cell surface
-Helps cell maintain cell shape Cilia are shorter and more numerous on cells
-Also help move organelles around Flagella are longer and fewer (usually 1-3) on cells
-Made of proteins  Vacuoles
 Microfilaments are threadlike & made of ACTIN -Fluid filled sacks for storage
 Microtubules are tube-like & made of TUBULIN -Small or absent in animal cells
 Centrioles -In plants, they store Cell Sap; Includes storage of sugars,
-Found only in animal cells proteins, minerals, lipids, wastes, salts, water, and enzymes
-Paired structures near nucleus Plant cells have a large Central Vacuole
-Made of bundle of microtubules  Chloroplasts
-Appear during cell division forming mitotic spindle -Found only in producers (organisms containing chlorophyll)
-Help to pull chromosome pairs apart to opposite ends of the cell -Use energy from sunlight to make own food (glucose) -Energy
 Mitochondrion (plural = mitochondria) from sun stored in the Chemical Bonds of Sugars
- “Powerhouse” of the cell -Surrounded by DOUBLE membrane
-Generate cellular energy (ATP) -Outer membrane smooth; inner membrane modified into sacs
-More active cells like muscle cells have MORE mitochondria called Thylakoids
-Both plants & animal cells have mitochondria  Thylakoids in stacks called Grana & interconnected  Stroma
-Site of CELLULAR RESPIRATION (burning glucose) – gel like material surrounding thylakoids
-Double Membranous
-It’s the size of a bacterium PROPERTIES OF WATER
-Contains its own DNA; mDNA 1. Capillary Action
-Its folded inner membrane called CRISTAE increases surface - is when water defies gravity
area for more chemical reactions; Interior called MATRIX 2. Adhesion
-Come from cytoplasm in the EGG cell during fertilization. - is when water bonds with other molecules other than itself
Therefore, you inherit your mitochondria from your mother 3. Cohesion
 Endoplasmic Reticulum - ER
- is when substances bond with themselves. Like when water bonds -Transport across the membrane that does NOT require energy
with other water molecules. This causes surface tension on the surface of a. Diffusion
the water, making organisms that live on the surface of the water able to -the transport or movement of molecules from higher concentration
live there to lower concentration without expenditure of energy
- causes steady stream of water because the water molecules are bonding - Molecules tend to spread out into the available space. Same thing
together. It will then turn into surface tension because of the puddle that happens across a membrane - IF that molecule can pass the
will form membrane
4. Specific Heat  When the concentration of molecules is different inside and
- is the specific temperature at which a substance boils at. For example, outside of the cell membrane, concentration gradient is established.
when sand is hot at the beach and water isn’t the same temperature as the Then the molecules moves from higher concentration to lower
sand. Without this property organisms that live in the water would die concentration until equilibrium is maintained. When the
because they are sensitive to specific changes concentration of molecules becomes equal on both side of the
5. Universal Solvent membrane, transport process stops. In some case, the molecules
- Water is a universal solvent because it can dissolve most substances. after entering the cell transform metabolically, preventing to build
Water dissolves things like salt and sugar. This is beneficial because it up concentration of transported molecules, hence the concentration
allows mixtures to be made. gradient remain established. The rate of diffusion is determined by
6. Density concentration gradient and permeability of cytoplasmic membrane.
- is how packed the molecules of something is. Ice is actually less dense Greater the concentration gradient and permeability of the cell
than water because water molecules expand when they freeze. This is membrane, greater will be the rate of passive diffusion.
beneficial because when the water freezes over, the organisms in the water  Particles, like solute, will always move from an area of high
will be able to survive. It also acts as an insulator concentration to an area of low concentration. This is called
7. Polarity moving down a concentration gradient.
-is the attraction between the hydrogen and oxygen atoms because the b. Facilitated Diffusion
hydrogen has a positive charge and oxygen has a negative charge. This -Some substances cannot diffuse straight across the membrane - go
is beneficial because it allows water to be created and without water, through a carrier protein - no energy is used because the molecules
we would not be able to sustain life are still moving from high concentration to low concentration -
glucose does this
MEMBRANES AND TRANSPORT c. Osmosis
Structure of the membrane: -The diffusion of water
-The movement of solvent (water) across membrane in response to
the concentration gradient of solute
 Isotonic solution
-two solutions have the same concentration of solute. Water move
equally in both directions inside and outside of cell.
 Hypertonic solution
-the solution has a higher concentration of solute than the solution it
is being compared to
-water moves out of the cell so that cell shrinks
 Hypotonic solution
-the solution has a lower concentration of solute than the solution it
is being compared to
-water moves inside the cell so that cell swells up
 Water will always move from a hypotonic region to a hypertonic
Made of: phospholipids, proteins and carbohydrate chains region through a semi-permeable membrane

Water Balance of Cells

Extracellular Matrix
 Plant cells - cell walls, made of cellulose fibers, are connected
through channels
 Animal cells - secrete a sticky coat called the extracellular matrix
- fibers made of the protein "collagen" hold cells together in
tissues
Membrane Function:
 Membranes are selectively permeable - they let certain
molecules into the cell, and keep certain things out Tonicity
 Membrane proteins play important roles in the cell membrane - - ability of a surrounding solution to cause a cell to gain or lose water
help regulate the flow of molecules in and out of the cell and 2. Active Transport
do much more! -Transport across the membrane that REQUIRES energy
-have 6 main functions: transport, enzymatic activity, signal -Proteins will pump molecules across the membrane, from low
transduction, cell- cell recognition, intercellular joining, and concentration to high concentration - against or "up" the concentration
attachment to the cytoskeleton ECM gradient
Membrane Transport Systems: Sodium-Potassium Pump
1. Passive transport
-is a structure known as a cell-membrane pump that uses energy to  Hydrochloric acid (HCl)
transport Sodium and Potassium ions in and out of the cell; Potassium -stomach acid
inside, Sodium outside  Sulfuric acid (H 2 SO 4 )
Bulk Transport -car batteries
-The movement of macromolecules such as proteins or polysaccharides  Boric Acid (H 3 BO 3)
into or out of the cell; large particles (or large quantities of smaller -Sea water
particles) are moved across the cell membrane  Oxalic Acid (H 2 C 2 O 4)
 Exocytosis (exo = external, cytosis = transport mechanism) -Wood cleaner
-is a form of bulk transport in which materials are transported  Phosphoric Acid: (H 3 PO 4)
from the inside to the outside of the cell in membrane-bound -Soft Drinks
vesicles that fuse with the plasma membrane. Cells must take in Base
certain molecules, such as nutrients, but they also need to release - substance that decreases the hydrogen ion concentration in a solution;
other molecules, such as signaling proteins and waste products, and usually possesses a large number of hydroxide ions
to the outside environment -turns litmus paper into blue in color
 Endocytosis (endo = internal, cytosis = transport mechanism) -takes protons
-is a general term for the various types of active transport that Types of Bases:
move particles into a cell by enclosing them in vesicle made out  Aluminum hydroxide (Al[OH] 3 )
of plasma membrane -antacids, deodorants
 Phagocytosis (literally, “cell eating”)  Ammonium hydroxide (NH 4 OH)
- is a form of endocytosis in which large particles, such as -glass cleaner
cells or cellular debris, are transported into the cell  Calcium hydroxide (Ca[OH] 2 )
 Pinocytosis (literally, “cell drinking”) -caustic lime, mortar, plaster
-is a form of endocytosis in which a cell takes in small  Magnesium hydroxide (Mg[OH] 2 )
amounts of extracellular fluid. -laxatives, antacids
 Sodium bicarbonate/sodium hydrogen carbonate (NaHCO 3 )
FLUIDS, ACIDS AND BASES -baking soda
 Sodium carbonate (Na 2 CO 3 )
-dish detergent
 Sodium hydroxide (NaOH)
-lye, oven and drain cleaner
 Sodium hypochlorite (NaClO)
-bleach
 Acetone (C3H6O)
-Paints and waxes
 Ammonia (NH3)
-Cleaning liquids
How Do Acids and Bases Affect Our Health?
 Acids and bases are used to help digest foods in our body, are
pH Scale found in the medicine we consume, and are found in many
-stands for “potential of Hydrogen” cleaning products
-is a scale used to measure the acidity of a substance.
 When the human body is digesting foods, gastric acids is used in
It is measured by a scale up to 14.
order to break down these foods. If your stomach produces
 If the substance falls within the measures of 1 till 6 it is an
excess amounts of gastric acid, then heartburn or acid reflux may
acid. The higher the concentration of hydrogen ions, the
occur.
more acidic it is.
 Cleaning products are mostly basic, and this property helps
 If it falls within the measures of 8 till 14 it is a base. The
strengthen the detergent’s cleaning power.
lower the concentration of hydrogen ions, the more basic it
is.  Acids and bases also help to balance the pH levels in our body,
 7 on the scale is neutral. and without balanced pH levels various health related issues may
Acid develop in our bodies.
-any compound that increases the number of hydrogen (hydronium  The balance of acids and bases in the human body also
ions) when dissolved in water contributes to homeostasis.
-turns litmus paper into red in color How Acidic Foods Affect the Body:
-gives proton  Brain- Neurological conditions like Alzheimer’s, dementia,
Parkinson’s and reduced mental clarity
 Hydronium ion (H₃O⁺)
 Lungs- Creates excess mucus in the body, manifesting as
-released when acid dissolves
coughing, breathing trouble, chest pain, fatigue and sinus issues
-the positively charged ion formed when Hydrogen ion combines
with water  Heart- Acidic plaques causing heart attacks, strokes, and
Types of Acids: cardiovascular disease
 Acetic acid (CH 3 COOH)  Liver/Kidneys- Most susceptible to acidic damage. Causes
-vinegar, acetate inflammation, ulcers, stones and cancer
 Acetylsalicylic acid (HOOCC 6 H 4 OOCCH 3 )  Stomach- Excess gas, nausea, indigestion, acid reflux, bloating,
-aspirin bad breath, belching
 Ascorbic acid (H 2 C 6 H 6 O 6 )  Bones- Strips our bones of crucial minerals like calcium to help
-vitamin C buffer acidic overload in body- results in brittle
bones and osteoporosis
 Carbonic acid (H 2 CO 3 )
-soft drinks, seltzer water  Intestines- Indigestion, reduced nutrient absorption (vitamin/
mineral deficiencies), bloating, candida
 Citric acid (C 6 H 8 O 7 )
-citrus fruits, artificial flavorings  Skin- Chronic acidosis results in eczema, acne, rashes, all
dermatitis types and random breakouts
Buffers
-solutions which can resist changes in pH when acid or alkali is added;
is typically composed of a weak acid and its conjugate base
3 Major Buffer Systems in the Body:
1. Carbonic Acid Bicarbonate Buffer
-most important buffer in plasma as it is the only one that is coupled to
the respiratory system
- Cellular respiration produces carbon dioxide as a waste product. This
is immediately converted to bicarbonate ion in the blood. On reaching
the lungs it is again converted to and released as carbon dioxide. While
in the blood, it neutralises acids released due to other metabolic
processes. In the stomach and deudenum it also neutralises gastric
acids and stabilises the intra cellular pH of epithelial cells by the
secretions of bicarbonate ions into the gastric mucosa.
2. Phosphate Buffer
-major intracellular buffer
- operates in the internal fluids of all cells. It consists of dihydrogen
phosphate ions as the hydrogen ion donor
(acid) and hydrogen phosphate ion as the ion acceptor
(base). If additional hydroxide ions enter the cellular fluid, they are
neutralised by the dihydrogen phosphate ion. If extra hydrogen ions
enter the cellular fluid, then they are neutralised by the hydrogen
phosphate ion
3. Protein Buffer
-helps to maintain acidity in and around the cells. Hemoglobin makes
an excellent buffer by binding to small amounts of acids in the blood,
before they can alter the pH of the blood. Other proteins containing
amino acid histidine are also good at buffering.

Acidosis
-when your body fluids contain too much acid
- is said to occur when arterial pH falls below 7.35
-for example, when you have diarrhea
Alkalosis
-when you lose too much acid and gain too much base
-for example, stomach acid is lost during periods of prolonged
vomiting