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Exam 1 Study Guide

by: Jennifer Scheuer

Exam 1 Study Guide BSC 114

Jennifer Scheuer

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this is the material covered on the first exam
The Principles of Biology 1
Dr. Stephenson
Study Guide
Biology, Water, carbon, Bonding, cells
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This 12 page Study Guide was uploaded by Jennifer Scheuer on Saturday September 17, 2016. The Study Guide belongs to BSC 114 at University of Alabama - Tuscaloosa taught by Dr. Stephenson in Fall 2016. Since its upload, it has received 289 views.


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Date Created: 09/17/16
BSC 114: Exam 1 Study Guide Atoms, Bonds, and Molecules I. Atomic Structure A. Atoms  Nucleus contains protons (+) and neutrons (no charge)  Electrons (-) orbit the nucleus B. Protons  Determines atomic number C. Neutrons  Number of protons + number of neutrons = atomic mass number  Isotopes: atoms with different number of neutrons D. Electrons  In an uncharged atom: number of protons = number of electrons  Ion: number of protons DOES NOT = number of electrons  Electrons occupy “orbits” or energy levels  First orbit: 2 electrons  Second orbit: 8 electrons  Third orbit: 18 electrons  Atoms are stable when their orbits are full, this can happen in two ways:  Covalent bonds: atoms share electrons  Ionization: atoms accept or lose electrons II. Elements, compounds, and molecules A. Element: only one type of atom (ex. Calcium, hydrogen, oxygen) B. Compound: two or more types of atoms in a fixed ratio (ex. Table salt) C. Molecule: two or more types of atoms held together by covalent bonds (ex. Water) III. Bonds A. Covalent Bonds  Valence: bonding capacity  Electronegativity: affinity for electrons (oxygen +nitrogen are very electronegative)  Polar covalent bond: unequal sharing of electrons, results in positive and negative poles  Non-polar covalent bond: atoms have similar electronegativity B. Ionization  Atoms gain or lose electrons  Cation: positively charged ion (lose an electron)  Anion: negatively charge ion (gain an electron) C. Non-Covalent bonds  Much weaker than covalent bonds  Hydrogen bonds: two polar molecules attracted by opposite charges  Ionic bonds: bonds based on charge attractions  Van der Waals forces: weak attractions between atoms that are close together Water IV. Properties of Water A. Cohesion + Adhesion  Cohesion: attraction of the same type of molecule (water- water)  Adhesion: attraction of two different molecules (water-polar molecule) B. Specific Heat + Heat of Vaporization  Specific Heat: amount of energy it takes to raise temperature  Water has a high specific heat  Calorie: energy needed to raise 1 gram of water 1 degree C  Heat of Vaporization: amount of energy needed to go from liquid to gas  Water has a high heat of vaporization C. Ice  Hydrogen bond lattice is fixed with crystalline structure  Ice is less dense than water so it floats D. Solubility  Polar and charged molecules dissolve in water (hydrophilic)  Non-polar molecules with no hydrogen bonds are insoluble (hydrophobic) V. Water Ionization A. Acids and Bases  In pure water H+ and OH- concentrations are equal  If H+ concentration is greater than OH- the solution is acidic  If H+ concentration is less than OH- the solution is basic  Acid: compound that ionizes to release H+ = increase H+  Base: compound that ionizes to release OH- or binds with H+ to reduce H+ concentration  Buffers: chemical that resists changes in pH  Absorbs H+ when H+ concentration is high and donates H+ when H+ concentration is low Carbon I. Carbon Chemistry A. Valence of four, does not ionize B. Carbon can make single, double, and triple bonds C. Can be linear, branched, or ring compounds II. Functional Groups A. Hydroxyl  Alcohols  O-H  Polar and hydrogen bonds B. Carbonyl  C=O  Polar and hydrogen bonds C. Carboxyl  Hydroxyl + Carbonyl  Acidic D. Amino (NH ) 2  Accepts H+ to become NH + 3  Basic E. Sulfhydryl  S-H  Protein structure  Two sulfhydryl make covalent bonds to cross link proteins F. Phosphate (PO )4  Valence of 5 (can make five covalent bonds)  Acidic  Makes DNA an acid G. Methyl (CH )3  Not reactive  Modifies structure and function of biological molecules III. Isomers A. Isomers  Compounds with the same chemical formula but different structures B. Structural Isomers  Different arrangement of covalent bonds C. Cis-trans/ Geometric Isomers  Different atom arrangement around a double bond  Cis=same sides  Trans= opposite sides D. Enantiomer  Different arrangement of atoms/groups around an asymmetric carbon (carbon bonded to four different things)  Chemical mirror images  Arrangement of –H and –OH at an asymmetric carbon causes different properties Biological Molecules I. Polymers A. Macromolecules: large molecules (long chains of similar subunit) B. Dehydration Reaction: hydroxyl group + hydrogen are replaced by a covalent bond  Releases water C. Hydrolysis: water molecule replaces a covalent bond, adding a hydroxyl + hydrogen  Ex. Digestion breaking down macromolecules II. Carbohydrates A. Sugar and Polysaccharides  Equal amounts of carbon and water B. Sugars  Simplest carbohydrate  Monosaccharaides  3,5, or 6 carbons  1 carbonyl group, remaining carbon bond to –OH and –H  Named according to number of carbons  Aldoses: carbonyl group is on a terminal carbon  Ketoses: carbonyl group is on an internal carbon  Disaccharides  Two monosaccharaides joined in a polymer  Glycoside linkage: covalent bond between sugars  Polysaccharides  Glycoside linkage  Branched/Unbranched  Properties determined by monosaccharaides and bond type  Ring sugars  Pentose (5) and hexose (6) circularize to form rings  Carbon atom that forms the ring is an asymmetric carbon that forms two different enantiomers III. Lipids A. Fats and Oils  Storage molecules  Glycerol: 3 carbon alcohol (every carbon has a hydroxyl group)  Fatty acid: linear hydrocarbon with a terminal carboxyl group  Fatty acids are joined to glycerol by a dehydration reaction  Most common have 16-18 carbons (C-H)  Triacylglycerol: 3 fatty acids attached to a glycerol  Saturated Fats: fats with all single bond fatty acids (straight)  Pack together tightly (solid at room temperature)  High melting point  Unsaturated Fats: oils with some double bonded fatty acids (bent)  Low melting point  Liquid at room temperature B. Phospholipids  Major component of membranes  2 fatty acids attached to a glycerol rd  3 glycerol carbon is attached to phosphate and a small polar molecule  Tail is hydrophobic C. Steroids  Hormones and a component of membranes (cholesterol)  Four attached rings (different steroids have different chemical groups attached to the rings) IV. Proteins A. General  50% of the dry mass of a cell  Polymer: protein or polypeptide  Monomer: amino acid B. Amino Acid  Amino group- (alpha carbon-hydrogen)-carboxyl group (acidic)  Alpha carbon is bonded to an R group ( 20 R groups = 20 different type of amino acids)  Peptide bond: binds amino acids by dehydration reaction between amino and carboxyl groups  Backbone repeats: N-C-C (R group extends from backbone) C. Structure  Primary Structure: order of amino acids in the polypeptide  Determined by gene instruction  One end has an amino group (n-terminus) and the other has a carboxyl group (c-terminus)  Secondary Structure: local interactions due to hydrogen bonds between N-H and C=O  Alpha helix: backbone makes a spiral (held togetthr by hydrogen bonds between groups of every 4 amino acid)  Beta pleated sheet: backbone makes waves (lie adjacent to each other connected by hydrogen bonds)  Tertiary Structure: overall 3D structure, interactions between amino acid and R groups  Globular: compact and roughly spherical protein  Fibrous: extended roughly linear protein  Protein folds determined by R group interactions, hydrophobic interactions (non polar R groups fold internally), and disulfide bridges (two cysteine amino acids form covalent bond)  Chaperonines: proteins that help other proteins fold into their shapes  Quaternary Structure: proteins interact with different polypeptides VI. Nucleic Acids A. General  Monomer: nucleotide (phosphate, sugar, base)  Monomers for DNA and RNA  Energy containing and regulatory molecules for ATP and GTP  Polymer: polynucleotide B. Sugar: pentose  Ribose: typical pentose sugar (RNA)  Deoxyribose: atypical (2 H’s on C rather than 1H and 1O) C. Nitrogenous base  Pyrimidine: single ring 4 carbons and 2 nitrogens  Purines: double ring 5 carbons and 4 nitrogens Tour of the Cell I. Basics of a cell A. Membranes  Barrier to passage to most molecules  Plasma membrane: encloses the entire cell (all cells have one)  Cytoplasm: inside of the cell B. Organism Classification  Eukaryotes: nucleus and other organelles (animals, plants, fungi, algae, protists)  External membrane (plasma membrane)  Internal membrane bound organelles  Prokaryotes: nothing inside (bacteria, archaea) II. Membrane bound organelles A. Nucleus  Contains genes, enzymes, and regulatory molecules  Membrane: nuclear envelope  Double membrane (outer membrane continuous with ER)  Membranes are fused at nuclear pores (important for transport)  Nuclear lamina: network of fibers on the inside of the inner membrane  Chromosomes: structures inside the nucleus that contain genes B. Smooth Endoplasmic Reticulum  Network of vesicles close to the nucleus  Lumen: interior of a vesicle  Function in carbohydrate metabolism, lipid synthesis, and detoxification C. Rough Endoplasmic Reticulum  Layers of flattened sacs  Ribosomes attach to the outer surface (roughness)  Involved in protein synthesis  Complexes of proteins located in the cytoplasm  Bound Ribosomes: attached to the outer surface of the rough ER  Free Ribosomes: not attached to the rough ER  First stage in the secretory pathway D. Golgi Apparatus  Flattened sac that are more compact and less extensive than rough ER  Transport vesicles fuse with cis face and leave from trans face  Protein processing and sorting (sorted according to destination) E. Lysosomes  Spherical organelles  Digestion of endocytosed partials and worn out organelles  Autophagy: damaged organelles are enclosed by vesicles which fuse lysosomes for digestion F. Vacuoles  Pump excess water from cell  Food vacuoles: product of phagocytosis  Central vacuole: mostly storage for plant cells G. Peroxisome  Roughly spherical with granular crystalline cone  Detoxification of alcohol and drugs/ break down fatty acid III. The Cytoskeleton A. Microtubules (largest)  Composition: hollow tubes composed of protein tubulin  Position in the cell: internal, appear to radiate from the centrosome  Function: organelle movement  Motor proteins move along microtubules using ATP from hydrolysis  Cilia: short and many  Flagella: long and few B. Microfilaments  Composition: rod composed of actin (globular proteins)  Position: usually peripheral in the cell  Function: cell motility and structure  Reinforce microvilli to increase surface area C. Intermediate Filaments  Composition: rope-like filaments composed of fibrous proteins  Position: all over the cell  Function: structural IV. Extracellular components A. Cell Walls  Provides main structural feature of plants  Components: cellulose, polysaccharides, proteins, and glycoproteins  Components secreted by cells into extracellular space B. Extracellular matrix  Structure: interlocked extracellular fibers  Synthesis: components secreted by secretory pathway  Function: mechanical strength V. Cell Junctions A. Plants  Plasmodesmata: holes in the cell walls B. Animals  Tight Junctions: specialization connects membranes of adjacent cells  Acts as a barrier to passage of fluid between adjacent cells  Desmosomes: mechanical cell to cell attachments, reinforced with intermediate fillaments  Gap junctions: cytoplasmic continuity between adjacent cells, molecule passage Membranes I. Membrane Structure A. Fluid Mosaic Model  Membranes composed of lipid bilayer and proteins B. Lipid Bilayer  Phospholipid structure  Fatty acid tail (hydrophobic)  Polar head (hydrophilic)  Amphipathic: molecules with both hydrophobic and hydrophilic region  Lipid Bilayer: double layer of lipids  Polar head groups on the periphery  Fatty acid tails: internal hydrophobic cone C. Membrane Proteins  Integral membrane proteins: float on top of the lipids  Trans membrane proteins: extend through the lipid bilayer  Typically span the bilayer multiple times  Peripheral membrane proteins  Not embedded attached to membrane components by bonds D. Membrane Fluidity: degree to which lipid/proteins move in the plane of the membrane (varies with lipid composition)  Unsaturated fats: high fluidity  Saturated fats: low fluidity  Cholesterol hinders phospholipid movement E. Permeability of lipid bilayer  Cross easily: non-polar molecules  Cross slowly: small polar molecules  Does not cross: large polar molecules and charged molecules F. Diffusion  Moves down concentration gradient (high to low)  Equilibrium: no net movement = equal concentration everywhere G. Osmosis: diffusion of water across a membrane  Osmoregulation: membranes allow passage of water prevents solutes  Solvent: liquid in which solute is dissolved  Hypotonic solution: solute concentration outside the cell is lower than inside  Hypertonic solution: external solute concentration is higher than internal  Isotonic: concentration is same both inside and outside II. Membrane Transport A. Passive transport: high concentration to low concentration  Diffusion: molecules move without assistance  Facilitated Diffusion: large polar/charged molecules cannot cross (requires transport proteins)  Channels: hydrophilic channel on inside of the protein  Carriers: hydrophilic space changes shape B. Active Transport: move against concentration gradient (ATP driven) C. Co-Transport: one solute moves down concentration gradient provides energy to move another against concentration gradient D. Bulk Transport  Exocytosis: small membrane bound vesicles fuse with plasma membranes  Endocytosis: engulfs nearby parts forming a new internal vesicle  Phagocytosis: cell engulfs a particle  Pinocytosis: cell engulfs small volumes of liquid  Receptor-mediated endocytosis: cell internalizes tiny secretions of membranes


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