Fundamentals of Biochemistry

Biochem 5721 – The Basics of Life

As a Biochemistry major, you’ll have the opportunity to participate in cutting-edge research, with guidance from a faculty mentor. Many of our students also complete internships and pursue employment in the chemical or biotechnology industries. These experiences will make you a more competitive candidate for admission to professional programs.

These notes are for the first week of material following Midterm 1. Covers 1st Law of Thermodynamics, work, heat, and heat capacity.

Physical Biochemistry I

Have you ever seen one of those pharmaceutical commercials that show someone who was sick or unhappy at the beginning of the video being happy and frolicking in a field after taking a miracle drug? While the person is portrayed being healthy and feeling great, a narrator will read a laundry list of side effects that seem to contradict the advertised benefits.

These are the kinds of experiments that a physical biochemist would do to understand how chemical structure influences physical properties of biological molecules. This course is an introduction to physical biochemistry and the techniques that are used to study them.

Students who take this course will get access to the FSU Physical Biochemistry Facility (PBIF), a state-of-the-art research instrumentation facility that provides training, consultation and access to instruments for studying structures, stabilities and interactions of macromolecules by optical and vibrational spectroscopy, electrophoresis, nuclear magnetic resonance and X-ray crystallography. 3 undergraduate credits and 3 graduate credit hours.


Thermodynamics is the study of energy and its conversion into other forms of energy such as heat. It also deals with the transfer of matter between systems. Thermodynamics covers all processes in nature that are not at equilibrium. Energy is transferred into a system by heating, compression and adding matter and out of a system by cooling, expansion and extracting matter.

A definite state of a thermodynamic system is defined by its intensive properties such as temperature, pressure and volume. A property may change its value between states, but the change in value depends on the system’s starting and final conditions, not the path it takes to get there. This concept is referred to as the law of conservation of energy.

Closed systems are generally considered to be at equilibrium, and the first law of thermodynamics states that energy can neither be created nor destroyed; it only changes form. The second law of thermodynamics states that the entropy of an isolated system tends to increase over time.


Enzymes are biological substances that catalyze chemical reactions so they occur faster than they would without them. They are primarily proteins, but some ribonucleic acid (RNA) molecules also act as enzymes. Enzymes make it possible for biochemical reactions to take place in living cells at a rate fast enough to support life.

Every enzyme has a specific 3D shape that determines how it will bind with its substrate. It also has a unique set of amino acids that determine how it will react with the substrate. The active site amino acid residues may form temporary covalent bonds with the reactioning molecules as part of the catalytic process, but these are not permanent binding interactions.

Enzymes often require non-protein molecules called cofactors to function. These cofactors bind to the enzyme at its active site and the entire complex is referred to as an apoenzyme or holoenzyme. Some disinfectants, such as chlorine, iodine, and iodophores, inactivate bacteria by binding to their enzymes. High temperatures, such as those used in autoclaving and pasteurization, denature enzymes.

Biochemistry of Proteins

Proteins are highly complex, organic molecules that perform a wide variety of vital organism functions including DNA replication, transporting substances across membranes, catalyzing metabolic reactions, and providing structural support to cells. Each protein begins as a linear chain of amino acids bound together by the sequence of peptide bonds created during protein biosynthesis. The amino acid sequence defines the protein’s primary structure, which is normally folded up into a specific three-dimensional shape known as a native conformation.

Only a small fraction of the possible protein sequences can adopt the correct, functional, native conformation. This remarkable result is a product of natural selection, which favors proteins that are stable and effective in performing their biological tasks.

Amino acid side chains have various chemical properties including nonpolar, water-fearing (hydrophobic) and polar, positively or negatively charged (hydrophilic). During protein folding, the peptide bonds between amino acids can be stabilized by hydrogen bonding with each other. The resulting structures are known as secondary and tertiary structure, and they are held together by multiple noncovalent forces including H-bonds, electrostatic interactions, disulfide bridges, and Vander Waals forces.

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