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What is Biochemistry
➢ Simplest Definition: “Chemistry of the living cell”
➢Uses basic laws of chemistry, biology and physics to explain
processes of living cells
➢Study of life at the molecular level.
Introduction to Biochemistry
ENGR. JEREMIAH EMIER VILLANUEVA

Why study biochemistry? Biotechnology

➢ Lead us to fundamental
understanding of life
➢ Understand important issues in
medicine, health and nutrition.
➢ Has led to greater molecular
understanding of diseases
➢ Diabetes
➢ Sickle cell anemia
➢ Cystic fibrosis

Three areas of study for Biochemistry Tools to study biochemistry

1. Structural and functional biochemistry – Chemical structures and
3D arrangements of molecules
2. Informational Biochemistry – Language for storing biological data
and for transmitting that data in cells and organisms.
3. Bioenergetics - The flow of energy in living organisms and how it
is transferred from one process to another.
➢ Know the chemical structures and reactivities of molecules that
participate in cellular reactions
➢ Know the biological function of cellular molecules
➢ Know how all of the pieces and different pathways fit together.
➢ Prerequisite knowledge on:
➢ Gen chem, org chem, biology

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How did we originate?

What are we made up of?

➢ Most biological compounds are made up of only SIX elements
➢CHONPS

➢ Only 31 elements occur naturally in plants and animals.

➢ All organisms have similar biochemical pathways
➢ All organisms use the same genetic code.
➢ There are limited number of molecular building blocks
(biomolecules) that make up larger macromolecules.

Lab synthesized organic compound Biomolecule Functional Groups

➢ Early 19th century: “vital forces” were forces unique only to living ➢ The reactions of molecules are based on the reactions of their
things. respective functional groups.
➢ Organic compounds cannot be reproduced in a laboratory. ➢ These functional groups are polar and their polar nature plays a
➢ 1828: Friedrich Wohler synthesized urea from ammonium cyanate. critical role in their reactivity.

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Quick Review
FUNCTIONAL GROUPS

4 Major classes of biomolecules

➢Carbohydrates
➢ Examples: glucose, fructose, sucrose
➢ Mainly used as sources of cellular energy

➢ Lipids
Macromolecules ➢ Commonly known as fats
➢Organic compounds that are not very soluble with water
➢ Used as sources of cellular energy
➢ Components of cell membranes

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4 Major classes of biomolecules 4 Major classes of biomolecules

➢ Amino Acids ➢ Other
➢ 20 natural amino acids in total ➢ Vitamins – organic compounds necessary for proper growth and
➢ Used as building blocks for proteins development
➢ Heme – Organometallic compound containing iron; important for
➢ Nucleotides transporting oxygen in your blood stream.
➢ 5 in total
➢ Used as building blocks for DNA and RNA precursorss

Polymers of macromolecules

Polymers of macromolecules
➢ Starch and Cellulose
➢ Polymers of glucose molecules that differ only by how the glucose monomers are
linked.

➢ Proteins/polypeptides
➢ Amino acid monomers linked together

➢ DNA
➢ Heteropolymer of monomeric nucleotides; storage of genetic information

➢RNA
➢ Same as DNA; involved in transfer of the genetic information encoded by DNA

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Biomacromolecules 2 basic classes of organisms

➢ Self-assembles into cellular structures and complexes
➢ Recognize and interact with one another in specific ways to
perform essential cellular functions (membranes, complexes of lipids
and proteins).
➢ Interactions are weak and reversible
➢ Molecules have three dimensions and shapes.
➢ Prokaryotes and eukaryotes
➢ Similar processes occur in ALL cells, including prokaryotes.
➢ Trivia: much of the biochemistry that we understand was first
uncovered in prokaryotic systems.

Difference between Eukaryotes and

Prokaryotes
➢ Main difference – existence of subcellular organelles (e.g. nucleus)

Quick Review
EUKARYOTIC CELLS

Animal vs Plant cells

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Parts of the animal cell

Cytoplasm/cytosol Cytoskeleton
➢ Viscous aqueous environment (NOT free flowing) ➢ 3-D matrix made up of protein fibers
➢ Contains small molecules, nutrients, salts, soluble proteins
➢ Functions to give cells shape, allows cells to move, guides internal
➢ 20-30% of cytosol is protein – very concentrated organelle movement.
➢ Major cite of cellular metabolism (e.g. glycolysis)
➢ Connects all organelles.
➢ Contains the cytoskeleton

➢ Cytoplasm – portion outside the nucleus

➢Cytosol – aqueous portion of the cell that lies outside the membrane-bounded
organelles

Nucleus
➢ Site of most DNA and RNA synthesis
➢ Storage of genetic information
➢ Bound by a double membrane
➢ Largest organelle

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Endoplasmic Reticulum (ER) Mitochondria

➢ Network of interconnected, closed, membrane-bounded vesicles ➢Have a double membrane (inner and
outer)
➢ Attached to cell and nuclear membrane ➢ Place where most oxidative energy
➢ Used for manufacturing, modification and transport of cellular production occurs
materials ➢ Powerhouse of the cell
➢ Two types ➢ Forms ATP – convert oxygen and
➢ Smooth ER – site of lipid synthesis nutrients to energy
➢ Rough ER – site of protein synthesis via ribosomes ➢ Small, typically the size of a bacterium
➢ Ribosomes – made up of RNA and proteins not bound by a ➢ Has a small DNA molecule like that of
bacteria
membrane

Mitochondria Golgi Apparatus

➢Endosymbiotic hypothesis ➢ Flattened vesicles of lipid/protein/sugar
➢ Because of the double membrane, size and presence of the ➢ Usually found near smooth ER and nucleus
genome, it is believed that they are descendants of a bacteria
that was engulfed by larger host cells billions of years ago. ➢ Involved in protein and fat processing and trafficking to other
organelles (e.g. lysosomes, plasma membranes) – Distribution
➢Trivia – A cell can have over 1000 mitochondria. Depends on the
need for energy.

Lysosomes
➢Internal sacs bound by a single membrane
➢ Responsible for degrading cell components that have become
obsolete for the cell or organism
➢ Internal pH (approx. 5)
➢ Enzymes in lysosomes degrade polymers into their individual
building blocks.

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REDOX reactions
➢ Photosynthesis trap light energy use it as driving energy for the
reactions. (Reduction)
➢ Respiration consume carbohydrates to make use of their energy.
(Oxidation)
Bioenergetics

Brief analysis of ATP Brief analysis of ATP

Spontaneity of Biochemical Reactions

Can life exist

thermodynamically?