An Introduction to Biochemistry and Cells Student Edition 5/23/14 Pharm. 304 Biochemistry Fall 2014 Dr. Brad Chazotte 213 Maddox Hall Web Site: Original material only © B. Chazotte

GOALS Re-familiarize yourself with chemical functional groups that are biologically important. Understand how biochemistry is understood from the basic forces affecting the interaction of atoms on up to the macromolecular structures of living organisms. Understand how biochemical reactions and biochemical structures form the basis for the living cell. Development an understanding of structure/function as a basis for understanding biochemistry and “life”.

STRUCTURE-FUNCTION!

Common Biochemical Functional Groups I Voet, Voet & Pratt 2013 Table 1.2

Common Biochemical Functional Groups II Voet, Voet & Pratt 2013 Table 1.2

Principle Areas of Biochemistry 1.Structural Chemistry: the components of living matter and the relationship of biological function to chemical structure. 2.Metabolism: the totality of chemical reactions that occur in living matter. 3.The chemistry of the processes and substances that transmit and store biological information (viz. Molecular Genetics).

Biochemistry: The chemistry of life The chemical and 3-D structures of biological molecules. The interaction of biological molecules with each other. The cell’s synthesis and degradation of biological molecules The cell’s use and conservation of energy. The mechanisms for organizing biological molecules and coordinating their activities The storage, transmission and expression of genetic information.

Lehninger 2000 Figure 2.4 Timeline of the Evolution of Life on Earth Evolution: is not directed towards a particular goal, i.e., random changes. requires some built-in “sloppiness”, i.e., adaptable to unexpected changes. is constrained by the past, i.e., new arises from the old is ongoing.

The “Scale of Life” Alberts et al., 2004 Figure 1.9 People tend to look from the large to the small. In biochemistry one wants to see how the “small” creates the “large”

Lehninger 2000 Figure 2.1 Universal Cell Characteristics Where does biochemistry “occur”?

Typical Animal Cell Voet, Voet & Pratt 2013 Fig 1.8

Lehninger 2004 Figure 1.7 Animal Cell Structures & Functions

Lehninger 2004 Figure 1.11 Cellular Structural Hierarchy

Cellular Internal Structures Alberts et al., 2004 Figure 1.7 Human skin cell seen via light microscopy Newt cell seen with DIC light microscopy

Cell Electron Micrographs Alberts et al., 2004 Figure 1.8Lodish et al., Figure 5.42

Cell Nucleus (Eukaryotes) Alberts et al., 2004 Figure 1.15 Site of genetic material Double membrane around nucleus Pores in membrane to allow movement of molecules

Lehninger 2000 Figure 2.12 Human Chromosome Alberts et al., 2004 Figure 1.16

Lehninger 2000 Figure 2.11 Nucleus and Nuclear Envelope

Lehninger 2000 Figure 2.9 Cell Endomembrane System Electron micrographs

Cell Organelles Rough ER: protein synthesis Smooth ER: lipid synthesis, drug and toxic compound metabolism Golgi: receives and often chemically modifies molecules made in ER directing them to other locations including the cell exterior. An asymmetric organelle, e.g. cis and trans sides Lysosomes: contain enzymes that digest proteins, polysaccharides, nucleic acids and lipids – cellular “recycling centers” Peroxisomes: vesicles performing a number of oxidative reactions to degrade amino acids and fats- produce free radicals that can damage the cell – thus isolated from cell Mitochondria: cell power plants; metabolic centers

Lehninger 2000 Figure 2.13Mitochondrion Alberts et al., 2004 Figure 1.17 Chazotte, 2002 MA04006_08.TIF

The Cytoskeleton Actin Filaments (SF) Microtubules (MT) Intermediate Filaments [Also seen here: Polyribosomes (R)] A dynamic structure responsive to the cell’s needs and the environment. Structures are built up from monomeric subunits.

Lehninger 2000 Figure 2.16a Cytoskeleton: Actin Filaments Stress Fibers Lehninger 2000 Figure 2.17 Actin – protein found in all eukaryotic cells. Monomers assemble in presence of ATP to form 6-7 nm filaments

Cytoskeleton: Microtubules Lehninger 2000 Figure 2.16ab Formed from  and  tubulins 22 nm hollow tube structure Undergo constant polymerization and depolymerization Other proteins move along microtubules using ATP as energy

Lehninger 2000 Figure 2.16c Cytoskeleton: Intermediate Filaments 8 – 10 nm filaments Several proteins involved in reversible binding Distribution subject to regulated changes Provide mechanical support

Lehninger 2000 Figure 2.18 Cell Organelle Transport

Lehninger 2000 Figure 2.19 The Cell’s “Molecular Motors” Use energy of ATP for protein to move on microtubule There is a polarity to movement on the microtubules – a particular protein will move unidirectionally

The Cytoplasm Is actually crowded, highly organized and dynamic. Filaments & organelles are dynamic Endomembrane system separates specific metabolic processes & provides surfaces for enzyme-catalyzed reactions Exocytosis & endocytosis provide paths between the cell interior and the surrounding medium

Lehninger 2000 Figure 2.22 Cellular Connections Animal cells Provide barrier between tissue & external environment Strengthen physical connections between cells Provide small reinforced openings between adjacent cells through which ions, electric currents, and small molecules can pass.

Extracellular Matrix The complex network of polysaccharides (e.g. glycosamineglycans) or proteins (e.g. collagen) secreted by cells that serves as a structural element in tissues and also influences their development and physiology.

End of Lecture Excellent Website for cell images by the American Society for Cell Biology: The Cell Image Library