BioChem Final Review PART I INTRODUCTION I Foundations of Biochemistry a Properties that distinguish organisms i High degree of chemical complexity and microscopic organization ii Systems for extracting transforming and using energy 1 Counteracts entropy moving towards disorder iii Functions for each component of an organism and regulated integration of functions iv Mechanisms for sensing and responding to external stimuli v Capacity for exact self replication and assembly vi Capacity to change over time via evolution II Cellular Foundations a The Cell i Plasma membrane defines the periphery of the cell barrier between the cell and the environment 1 Composed of lipid and protein molecules that form a hydrophobic barrier around the cell 2 Allows passage of charged polar particles receptor proteins and enzymes 3 Incredibly flexible can grow with the cell by adding additional lipid and protein molecules 4 Never loses membrane integrity never a hole ii Cytoplasm 1 Composed of an aqueous solution called the cytosol a Cytosol is concentrated with enzymes and RNA molecules component molecules amino acids nucleotides etc metabolites small organic molecules coenzymes inorganic ions ribosomes and proteasomes which degrade proteins iii Nucleus 1 Stores the genome composed of DNA a Eukaryotes have a membrane separating nucleus from cytosol called nuclear envelope b Prokaryotes have no double membrane b Cell Size Limits Diffusion i Smallest cells have a volume of 10 14 mL ii Upper limit of cell size is due to rate of diffusion of solute molecules c Three Distinct Domains i Archae Bacteria and Eukarya 1 Archae and Bacteria Classifications a Aerobic vs Anaerobic i Obligate Anaerobes oxygen is poisonous ii Facultative Anaerobes ambidextrous b Energetic Classification i Phototrophs use sunlight 1 Autotrophic or heterotrophic ii Chemotrophs oxidation of chemicals 1 Autotrophic or heterotrophic iii Organotrophs use organic compouds d Membrane Bound Organelles of Eukarya i Mitochondria energy production ii Endoplastic Reticullum transport and ribosome synthesis iii Golgi complexes packaging and transport iv Peroxisomes used for breakdown of fatty acids v Lysosomes breakdown everything else vi Separated by fractionation 1 Fractionation using many different staged centrifuge speeds to separate out components of the cell by density to isolate these components e Cytoskeleton i The three dimensional mesh of protein filaments that forms the skeletal structure of a eukaryotic cell ii Contains three types of filaments differing in width composition and function 1 Actin filaments used for locomotion 2 Microtubules used for locomotion 3 Intermediate filaments f Supramolecular Structures iii Endomembrane system segregates specific metabolic processes and provides surfaces for reactions 1 Exocytosis transports materials out the cell via membrane fusion and fission used for secretion 2 Endocytosis transports materials into the cell via membrane fusion and fission used for extracellular uptake ingestion i Differ greatly in size from just 0 5 nm to 1 m ii Subunits of proteins nucleic acids and poly saccharides are joined by covalent bonds iii Supramolecular structures are held together mainly by weaker non covalent bonds hydrogen bonds between polar groups ionic interactions hydrophobic among nonpolar groups in aqueous solution and van der Waals interactions London forces III Chemistry Foundations a Carbon in Biomolecules i Carbon s Bonding Capacity 1 Carbon can form single bonds with hydrogen atoms 2 Forms doubles bonds with oxygen and nitrogen 3 Forms stable single bonds with up to four 4 other carbon atoms 4 It can also share double bonds with two other Carbon atoms or a triple bond with another Carbon atom ii Structure of bonds 1 Four single bonds with other carbon atoms forms a tetrahedron with bond angles of 109 5 2 This formation allows for free rotation depending on the functional groups that are attached 3 Double bonds are shorter than single bonds iii Functional Groups 1 All biomolecules are derivatives of hydrocarbons 2 Functional groups replace hydrogen atoms 3 Most common are alcohols amines aldehydes ketones and carboxylic acids 4 Many are polyfunctional more than one functional group with unique chemical characteristics and reactions b Universal Set of Small Molecules i Primary metabolites small organic molecules in every cell 1 Includes amino acids nucleotides sugars carboxylic acids and derivatives of each of the listed molecules 2 Generally polar water soluble and present in very small concentrations ii Secondary metabolites 1 Metabolites that are not present in every cell but are rather unique to certain types of cells a Ex Nicotine morphine quinine and caffeine in plants 2 Entire collection of small molecules is known as metabolome c Macromolecules i Major constituents of cells polymers assembled from simple precursor molecules 1 Shorter polymers are called oligomers 2 Proteins nucleic acids and poysaccharides are examples ii Proteins sum of all is called the cell s proteome 1 Polymers of amino acids 2 Compose largest fraction of the cell besides water 3 Some have catalytic activity function as enzymes 4 Also can be structural elements signal receptors or transporters 5 Most versatile biomolecule iii Nucleic acids 1 Store genetic material in the form of DNA and RNA 2 RNA molecules can have both structural and catalytic roles iv Polysaccharides 1 Polymers of simple sugars such as glucose 2 Three main functions a Sources of energy contain large amounts of energy b Rigid structural components of cell walls v Lipids c Extracellular recognition elements can be located on proteins or on cell surface to provide signal 1 Water insoluble hydrocarbon derivatives 2 Structural components of membranes phospholipid bilayer 3 Energy rich fuel sources 4 Can act as pigments and intracellular signals vi Proteins and nucleic acids are considered informational macromolecules d 3 D Structure Configuration and Conformation i Stereochemistry the arrangement of a molecule s constituent atoms in three dimensional space 1 Important in determining the function of a biomolecule 2 Many Carbon containing compounds exist as stereoisomers molecules with the same chemical bonds and components but with different configurations spatial layouts 3 Interactions between biomolecules are stereospecific they require specific configurations to carry out their functions ii Stereochemistry can be determined based upon 1 The existence