Outline: Biochemistry Prelim Exams

WEEK 1: INTRODUCTION TO BIOCHEM

1500s Why cells are alive? (curiosity)

1590  First glimpse of biochemistry
 Invention of microscope
 Zacharias Jannsen - invented microscope
 Hans Jannsen - his father
 Robert Hooke - improved and upgraded
microscope
1903 Biochem was coined by Carl Neuberg (german
chemist)
1800s Complete attempt to describe all matter in terms of
atoms and their properties

John Dalton - atomic theory

1900s  Complexity inside of a cell
 we will never understand what makes
organisms alive
1930  Erwin Schrodinger - radical idea
 All of the things that we see in biology have
their roots in molecules
 First foundation of a discipline (molecular
biology)
1953  James Watson and Francis Crick stole data from
Rosalind Franklin about the structure of DNA
1600s  Animalcules = little animals
 Animalcule are now called bacteria
1869  Friedrich Miescher - founder of DNA (swiss
researcher)
Atoms  Smallest unit of ordinary matter
 Composed of protons (+) and neutrons (no
charge)
3 constituent parts:
Protons - carries positive charge
Neutrons - neutral
Electrons - negative charge

Emergent properties  Biological molecules come together and

interact = new and properties emerge
 property which a collection or complex system
has, but which the individual members do not
have
 Micro organisms - bacteria
 Animalcules = little animals; Antonie Van
Leeuwenhook
Gregor Mendel  Founder of genetics - explained molecules
 Used “pea plant breeding” - traits can be
inherited
ATOMS - CHNOPS  Carbon 18%
 Hydrogen 10%
 Nitrogen 3%
 Oxygen 65%
 Phosphorus 1.2%
 Sulfur 0.8%
Molecule Atoms bonded together = biological molecules

4 molecules (CLPN)  Carbohydrates

 Lipids
 Protein
 Nucleic acid

2 types of nucleic acid  DNA - deoxyribonucleic acid

 RNA - ribonucleic acid

Cells  Biological molecules interact with each other =

cell emerges
 Smallest living structure
 Within cell, there is a diverse set of chemical
reactions that keep us alive
2 types of cell  Prokaryotic (no nucleus)
 Eukaryotic (has nucleus)
Biochemistry  Chemistry of life
 Study of chemical properties and process
occurring in living matter
Life sciences:  Genetics
 Immunology
 Physiology
 Pharmacology
 Pathology
 Basic sciences

Med science  Health - all molecules needed for the optimal

functioning of the body
 Disease - abnormalities in biomolecules (quality
or quantity)

2 major concerns in health sciences  Understanding and maintenance of health

 Understanding of effective treatment of
diseases

Wide, two-way street  Nucleic acid - genetic diseases

 Protein - sickle cell anemia
 Lipids - astherosclerosis
 Carbohydrates - diabetes mellitus

Sickle cell anemia  Lack of rich oxygen blood

 Vessel was clogged by cholesterol
 Affects the molecules in your RBC
 Result of ammunition in betahemoglobin
 Long chain, inflexible
 Causes blockage which doesn’t receive ample
amount of oxygen and RBC
 Might cause stroke
 Stiff and angular
Astherosclerosis  Vessel is clogged by cholesterol

Normal RBC  Compact and flexible

 Can squeeze through capillaries
Nucleic acid (RNA) (DNA)  Carry genetic info
Proteins  Consist of amino acid

Lipids  Fatty compounds that are insoluble in water

Carbohydrates  Naturally occurring compound

Energy yielding nutrients  Carbohydrates

 Fats
 Proteins

Cell macro-molecules  Proteins

 Polysaccharides
 Lipids
 Nucleic acid

Energy-poor end products H2O

CO3
NH3

Anabolism  produces complex molecules from simple

substances.
 Growth and building
 Ana = frozen = build a snowman lol

Catabolism  Cut or break down

 what happens when you digest food and the
molecules break down in the body for use as
energy. Large, complex molecules in the body
are broken down into smaller, simple ones.
 An example of catabolism is glycolysis.

Anabolism 2 metabolic processes

Catabolism
CELLULAR FOUNDATION OF BIOCHEMISTRY

15 to 20 billion years ago Universe arose as cataclysmic eruption of hot,

energy rich subatomic particles

Hydrogen and helium Simple elements were performed within seconds

4.54 billion years Earth was formed

Chemicals  Nitrogen
 Nitrogen oxide
 Carbon dioxide
 Methane
 Ammonia
 Hydrogen
 Hydrogen sulfide

Protobiont Collection of chemicals trapped within

membranes

Prokaryotes  First living organism

 Arose between 3.9 and 3.5 billion years ago

Cyanobacteria  Earth’s first photosynthesizers

 Appeared 2.4 billion years ago, set the stage
for a remarkable transformation

Start of multicellular life: eukaryotes  Evolved by a process called endosymbiosis

Endosymbiosis  Symbiotic relationship where one organism

lives inside the other
 Allowed much more complexity

1.5 billion years ago start seeing a multi-cellular eukaryotic organisms,

in the fossil record (ALGAE)

Sponges  Earliest animals

Food chain Ecosystem is structured by feeding relationships

FEATURES OF LIVING ORGANISM: MRS.C.GREN  Movement

 Respiration
 Sensitivity
 Control or homeostasis
 Growth
 Reproduction
 Excretion
 Nutrition
CELLS: THE BIO IN BIOCHEMISTRY

Cell membrane Cells share common components

Cytoplasm
DNA

Prokaryotic and eukaryotic cell Categories of cell

Eukaryotic cell Membrane bound nucleus

Prokaryotic cell Don’t have nucleus

Organelles  Little organs
 Specialized parts of the cell with unique jobs
to perform

Nucleus  Largest organelle

 Contains cell’s genetic material (DNA)
 Control center
 Mayor’s office of the cell

Mitochondria and chloroplast We can find trace amount of DNA

Mitochondria  Releases ATP
 Powerhouse of the cell
 Where the energy in the form of ATP is
produced

Ribosomes  Where proteins are made

 Does not have a membrane
 Found in cytoplasm
 Attached in rough er
 Factories of the cell

Endoplasmic reticulum  Net like system

 Production, folding, quality control and
dispatch of proteins
 Transport system
 smooth type: lacks ribosomes
 rough type: ribosomes embedded in surface
Golgi bodies  Flattened membrane sac
 Protein packaging
 Moves material in and out of the cell
 Trafficking, processing and sorting of newly
synthesized proteins and lipids
 JNT express of the cell

Microbodies  Small compartment surrounded by single

membrane
 Contain high concentration of enzymes

Lysosomes  Suicidal bags

 Contains enzymes that degrade polymers in
monomeric sub-unit
 Degrades and destroys aged or defective
organelles
  Police officer of the cell

Peroxisomes  Class of small membrane-bound organelles

 Contains large amount of “catalase”
 Degrades fatty acids and amino reactions
which produces H202 (Hydrogen peroxide)

 CHLOROPLAST 3 C’s that differentiate the cells

 CELL WALL
 CENTRAL VACUOLE

Chloroplast  Where photosynthesis occurs

 Found in plants
 Contains green chlorophyll

Cell wall  Structural support and protection

 Only in plants and bacteria
 Made of cellulose

Central vacuole  Stores water, food and waste

 Pushes the content of the cell toward the
membrane

Hypertonic condition  Less solute inside = more solute outside

 Solute cannot pass through plasma
membrane = water will move outside the
cell to balance the environment
 High to low concentration

Hypotonic condition  More solute inside = less solute outside

 Water will move inside the cell to balance
environment

Isotonic condition  Equal solutes inside and outside the cell

 Water will not move

Cytoskeleton  Provide support

 Help cell move
 Pulls chromosomes apart during mitosis

MICROFILAMENT (RED) 3 FUNCTIONS OF CYTOSKELETON

INTERMEDIATE FILAMENTS
MICROTUBULES (GREEN)

Microfilament (Red)  Fine thread like protein fibers

 Hold organelles in place
 Assist with cell movement
 Composed of protein called “actin”

Actin works in myosine

Intermediate filament  Maintaining cell shape
 Enables cell to withstand the mechanical
stress that occurs when cells are stretched
 or compressed
Ex. RBC

Microtubules (green)  Largest filament

 Work as highways for proteins
 Help pull chromosomes apart during mitosis
 Help movement with movement of the
entire cell (flagella or cilia)

WATER AND ITS LIFE SUSTAINING PROPERTIES

Water  Only substance on all of our planet

 Occurs naturally in solid, liquid and gas form
 Amazing solvent
 Highest cohesion of non-metallic liquid
 High surface tension
 Has specific heat

71% Surface of the earth

75%-95% Inside a living cell depending on the organism

60% Human body

80%-90% Inside other organisms

Ex. Fish and plants

H2O Hydrogen is partially positive

HYDROGEN AND OXYGEN Non-metal or gas

Covalent bond Sharing of electrons between 2 or non-metal

Polar 2 opposite ends of molecule

Hydrogen bonding An emergent property

Cohesion Attraction between two like things

Surface tension property of the surface of a liquid that allows to

resist an external force

Adhesion Attraction between two different substances

(opposite)

Capillary action  Movement of water within the spaces

 Adhesion, cohesion and surface tension
results to CA

Transpiration Process by which plants give off water vapor

through openings in their leaves

Hydrophilic substances  Water loving

 Polar with negative and positive charge
  Polarity is stronger than the cohesive forces
of water
 Strong enough to break all hydrogen bonds
of water

Hydrophobic substances  Water fearing

 Non-polar
 Molecules lack charged poles
 Do not dissolve in water

Water has a high specific heat  takes a lot of energy for water to evaporate
— going from a liquid to a gas (water
vapor). Still because of water’s extensive
hydrogen bonding.
 Water molecules have to first be broken
free of their hydrogen bonds before they
can start vibrating faster and have a higher
temperature.
 Eventually will reach 100 degrees Celsius
and evaporate out of the liquid phase to the
gaseous phase.
Evaporative cooling allow a thin film of water to coat our skin, and
when that water reaches a high enough
temperature, it evaporates.

SOLID WATER IS LESS DENSE THAN LIQUID ODD PROPERTY OF WATER THAT SUPPORTS LIFE
WATER
Ice density  The solid form is generally denser than the
liquid form.
 This is NOT the case for water.
 When the molecules cool down and slow
down even more, and water becomes ice—
a strange occurrence.

Hydrogen bonding in ice creates an open lattice
 More space is more air
 Unusual property of water supports life by
providing additional habitats for living
organisms.
 Ice also acts as an insulator and protects life
in small bodies of water like ponds and lakes
during winter.
 IF ICE SINKS – underwater is devoid of life
kay madatugan.

Properties of water
⚬ Cohesion
⚬ Surface Tension
⚬ Adhesion
⚬ Universal Solvent
⚬ High Heat Capacity
⚬ High Heat of Vaporization
⚬ Ice Density