BIOL 3510 1st EditionExam # 1 Study Guide Lectures: 1 - 8Lecture 1 (August 26)A solitary cell is the simplest form of life. Cell Theory: cells are the fundamental units of life. All present-day cells are believed to have evolved from an ancestral cell that existed more than 3 billion years ago. All cells grow, convert energy from one form to another, sense and respond to their environment, and reproduce themselves. All cells make use of the same types of biomolecules, and all use energy. All cells are enclosed by a plasma membrane that separates the inside of the cell from the environment. All cells have an ability to maintain internal stability, homeostasis. Allcells contain DNA as a store of genetic information and use it to guide the synthesis of RNA molecules and of proteins.Mutations are mistakes in the DNA that change the genetic plan from the previous generation and are the raw material for evolutionary change. Hooke studied dead cork cells in 1665. Cell Biology was born after Schleiden in 1838 found that plants were made of cells, and Schwann in 1839 who found the animals were made of cells also.Schleiden and Schwann’s Cell Theory – all living things are formed by the division of existing cells.Magnification is the enlargement of the physical appearance of something. Resolution is the ability to distinguish two separate points. 0.2mm is the minimum resolvable by the unaided eye.Smaller needs light microscopy, SEM or TEM.Light Microscopy = 0.2 mm – dead or alive transparent, thin samples with stainingFluorescence Microscopy = 0.2 mm – 1st filter narrows wavelength, 2nd blocks othersTransmission Electron Microscopy (TEM) = 2 nm - Electrons and magnets are used to create and focus the image, dead samples are sectioned and stained with electron dense materials to create contrastScanning Electron Microscopy = 3-20 nm - Heavy metal-coated, dead samples are scanned by anelectron beam, pattern of electron scatter generates a 3D-like imageProkaryote: Greek derivation meaning “before the nucleus” Single-celled organisms. Is divided into two domains: bacteria and archae, the most diverse and numerous of cells on Earth, with no membrane-bound organelles. Eukaryote: Contain a well-defined nucleus surrounded by a nuclear membrane, can be single-celled, such as yeasts and Paramecium, or multi-cellular, such as animals and plants, with membrane-bound organelles, no peptidoglycan if cell wall even present, and size: may be 10x largerModel organisms: reproduce rapidly, are convenient for genetic manipulation, others are multicellular and transparent so we can watch the development of all their tissues and organs, ability to grow under controlled conditions.Molecular biologists have focused on E. coli. Brewer’s Yeast is a simple eukaryotic cell. Arabidopsis has been chosen as a model plant. Model animals include flies, fish worms, and mice. Biologists also directly study human beings and their cells. Comparing genome sequences reveals life’s common heritage.Lecture 2 (August 28)Proteins are composed of chains of amino acids linked together by peptide bonds. Amino acids can be grouped by their side chains. Peptide bonds are covalent bonds (90 kcal/mol in water or vacuum) where electrons are shared unequally in a polar covalent bond. Polar covalent bonds create dipoles within a molecule due to unequal electron distribution. Peptide bonds form via condensation reactions. The conformation of a protein is specified by itsamino acid sequence. 3D shape is inherent. 4 levels of protein structural organization: primary, secondary, tertiary, quaternary.4 Types of Non-Covalent Bonds/Forces in Cells1. Electrostatic attractions (3kcal/mol) forces that attract oppositely charged atoms2. Hydrogen bonds (1kcal/mol) a weak bond between an electronegative atom and a hydrogen bound to another electronegative atom3. Van der Waals interactions (0.1 kcal/mol) fluctuations in the electron cloud surrounding an atom creates a transient dipole. This dipole induces an opposing dipole in a nearby atom generating an attraction4. Hydrophobic forces (not really a bond) exclusion of non-polar surfaces from the hydrogen-bonded water networkChaperones are proteins that improve the efficiency of protein folding in cells. Hydrogen bonds between polypeptide backbone groups create secondary structures.Alpha-helix: Polypeptide twists to form a cylinder. Stabilized by H-bonds between a C=O (n) and a N-H (n+3). Often found in proteins that span membranes. 2 or 3 of them wrapped around each other form a stable coiled-coil. Beta-sheet: Stabilized by h-bonds between the C=O and N-H groups on adjacent lengths of a polypeptide chain. Alternate R groups extend in opposite directions. Can be parallel or anti-parallel. Often form the core of stable proteinsIntrinsically disordered sequences correspond to unstructured regions of some proteins. The final 3D conformation of single polypeptide is the tertiary structure, held together mostly by non-covalent bonds. Quaternary structure is the binding of two or more polypeptides to form a single complex, held together mostly by non-covalent bonds/forces.Protein domains are regions of a polypeptide chain that fold independently into a stable structure. They can be combined to create proteins with new functions. Disulfide bonds are covalent bonds between cysteines that act as “atomic staples” to stabilize extracellular proteins.X-ray crystallography is used to determine the 3D structures of proteins. Nuclear magnetic resonance (NMR) spectroscopy is used to determine the 3D structure of small protein.Lecture 3 (September 2)Proteins interact with other molecules. Ligand: anything bound by a protein. Binding site: area of a protein that interacts with a ligand – selective binding is mediated by many, non-covalent bonds/forces. Proteins have diverse functions such as: speed up the rate of chemical reactions (enzymes), provide support in and outside of cells (like keratin), and function in storage and transport (like hemoglobin). Enzyme: protein that acts as a catalyst.The substrates (ligand) binds to an active site (binding site). Substrate is altered upon binding so that the desired reaction is favored: 1) Holds substrates in alignment: envourages reaction, 2) Re-arranges electrons: stabilizes intermediates, 3) Alters bond angles: moves towards transition state. Allosteric proteins undergo conformational changes upon ligand binding which alters their activity. Feedback