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BIO 1020 Final Exam
Ch. 16, 17, Exam I and II Cards
| Term | Definition |
|---|---|
| Chemical Bonds | Attractions holding atoms close together, caused by transferred / shared valence electrons |
| Cation | Positively charged ions |
| Anion | Negatively charged ions |
| Ionic Bond | Attractions between a cation and anion |
| Ionic Compounds | Salts |
| Covalent Bonds | Strongest bonds within organisms |
| Van Der Waals Interactions | Attractions between molecules close together as a result of asymmetrically distributed electrons in molecule / atoms, resulting in "hot spots" of positive and negative charge |
| Single Bond | Sharing one pair of valence electrons |
| Double Bond | Sharing two pairs of valence electrons |
| Structural Formula | H-H |
| Molecular Formula | H2 |
| Molecule | Two or more covalently bonded atoms |
| Molecular Shape (Interact, Recognize, Similar) | Recognize and interact with each other with specificity. Similar shapes result in similar biological effects |
| Chemical Reactions | Making or breaking of chemical bonds |
| Chemical Equilibrium | Forward and reverse reaction rates are equal |
| Energy Coupling | Use exergonic reactions to drive endergonic reactions, mediated by ATP |
| ATP | Does work by hydrolysis / breaking the phosphate bond / phosphorylation, it is renewable |
| Open V. Closed System | Matter and energy is exchanged with the surroundings v. only energy exchange |
| Localization of Enzymes | Some enzymes are in specific organelles and within specific areas in organelles |
| Feedback Inhibition | The en product of a metabolic pathway shuts down the pathway, feedback promotion is when the product influences another reaction |
| Cooperativety | Allosteric regulation amplifies enzyme activity, binding a substrate to active site stabilizes a favorable shape |
| Three Controlling Tactics of Enzymes | Inhibition (competitive and noncompetitive control), pH/ temperature, genetic control (not making any more) |
| Noncompetitive Inhibitors | Bind to another part of an enzyme (toxins, poisons, antibiotics) |
| Competitive Inhibitors | Bind to the active site (toxins, poisons, antibiotics) |
| Allosteric Regulation (made of, forms) | Inhibit or stimulate enzyme activity, mostly polypeptide subunits, each enzyme has active / inactive forms |
| Coenzyme | Organic cofactor, vitamins (B12, C) |
| Cofactors | Nonprotein enzyme helpers (Fe+, Zn+, Mg+, Mn+), hold onto molecule |
| pH | Effects enzyme, lysosomes change pH environment |
| Active Site (job) | Region on enzyme where substrate binds, orients substrate, strains bonds, provides favorable microenvironment, bonds to substrate |
| Induced Fit | Substrate brings chemical groups in activation site into positions that enhance the reactions |
| Enzyme-Substrate Complex | Enzyme bound to substrate |
| Substrate | Reactant enzyme acts on |
| Enzymes Lower Activation Energy Barrier | Induced fit bends / breaks bonds E + Substrate -> ES -> E + product |
| Equilibrium | Cells don't have, too many reactions |
| Endergonic Reactions | Absorbs free energy, take up heat, coupled with exergonic. i.e.: making ATP |
| Exergonic Reactions | Net release of energy, release heat, coupled with exergonic. i.e.: cellular respiration |
| Chemical Energy | Potential energy for release in reactions (glucose, food) |
| Anabolic Pathways | Build molecules, absorb energy, dehydration synthesis |
| Catabolic Pathways | Break down molecules, release energy, hydrolysis |
| Metabolic Pathway | Steps to get product, coordinated sequence allowing efficiency / control, run by enzymes |
| Metabolism | Totality of organism's chemical reactions |
| Bulk Transport (Receptor-Mediated, Ligand) | Via vesicles, requires energy, phagocytosis (eating), receptor-mediated (binding of ligand triggers vesicle formation) ligand- molecule binding to receptor |
| Cotransport | When active transport of solute directly drives transport of another |
| Active Transport (Electrochemical Gradient) | Against concentration gradient, requires ATP Electrochemical Gradient- voltage difference across a gradient (proton pump) |
| Passive Transport (Do channel proteins change?) | Facilitated diffusion with a concentration gradient by channels, no energy, only change in shape of protein |
| Passive Transport (Osmosis) | Diffusion with concentration gradient Osmosis- H20 is solvent |
| Transport Proteins (Pores, Carrier Proteins, Molecules must be…) | Allow passage of hydrophilic substances, channels / compartments / pores made of selective proteins, carrier proteins bind to molecules and change shape |
| Osmoregulation | Control of water balance |
| Water Balance (Tonicity, Isotonic, Hypertonic, Hypotonic) | Ability of solution to cause water loss / gain No net water movement Solute concentration is greater outside, cell loses water Solute concentration is greater inside the cell, cell gains water |
| Selevtive Permeability (Hydrophobic and Polar Molecules) | Materials exchange by proteins / lipids that determine what can pass, hydrophobic (hydrocarbon i.e.: hormones) pass membrane rapidly, polar molecules (sugars) don't cross easily |
| "Sideness" of Membranes | Have distinct inside / outside faces that are asymmetrical |
| Cell-Cell Recognistion / Communication (what are receptors made of?) | Receptors, glycolipids / proteins, carbohydrates on external side (transported from golgi) |
| Six Major Functions of Membrane Proteins (Joining) | Transport, enzymatic activity, signal transduction, cell-cell joining, intercellular joining, extracellular joining |
| Membrane Proteins | Peripheral proteins (bound) and integral proteins (penetrate), hydrophobic regions |
| Cellular Membranes | Selectively permeable, amphipathic molecules, fluid mosaic model, structural and functional, lateral movement |
| Microvilli | Projections increasing cell surface area |
| Centrosome | Ancre point for microtubules, contains centrisomes |
| Cytoskeleton (Structures, Roles) | Microtubules, microfilaments, intermediate filaments. Support / maintain shape, motility with motor proteins, vesicle travel, regulate biochemical activities |
| Mitochondria (Functions,Contains, Structures) | Site of cellular respiration, make ATP, contain own DNA (not enough for life), Cristae- folded inner membrane, mitochondrial matrix |
| Peroxisomes (What is it? Functions) | Metabolic compartments, stores enzymes used to break down hydrogen peroxide |
| Chaperonins / Protiosomes (Associate with?) | Protein molecules assisting proper filing of other proteins, make sure certain proteins join properly, associate with ribosomes, creates ultimate environment, protiosomes degrade incorrect proteins |
| Denaturation | Break of Secondary-Quaternary Structure, alterations in pH, salt concentrations, temperature, and others cause proteins to unravel, renaturation can be difficult |
| Disulfide Bridges | Hold permanent shape in Tertiary Structure of proteins, only covalent polypeptide bond |
| Secondary Structure | Alpha-helicies, beta-sheets, refers to directions of bonding |
| Primary Structure (How determined?) | Sequence of amino acids, inherited by genetic information |
| Amino Acids (How linked? Different Properties) | Carboxyl and amino ® groups, properties due to differing R groups, linked by peptide bonds with dehydration synthesis |
| Proteins (Function, Structure) | Structural support, storage, transport, cellular communication, movement, and defense, one or more polypeptides |
| Quaternary Structure (Structure) | Two or more polypeptide chains form one macromolecule, coiled coils, strong |
| Tertiary Structure (Bonds, Ends) | Hydrogen bonds, ionic bonds, hydrophobic interactions, and Van Der Waals Interactions between R groups that are a part of amino acids, N-terminus / C-terminus (NH and COOH groups on end of chains) |
| What makes membrane selective? How is it a fluid mosaic of function? | Amphipathic phospholipids, structure, proteins Different proteins with different functions that float around side by side |
| Endomembrane System (Functions, Transport) | Complex factor of compartmental organization, transport proteins by budding |
| Endoplasmic Reticulum (Types, Functions) | Smooth- lack ribosomes, adds to membrane, makes glycoproteins / glycolipids, sends directions Rough- With ribosomes, transports proteins going out of the cell / to the membrane, secretes glycoproteins, distributes transport vesicles |
| Golgi Apparatus (Function, Structure) | Modifies proteins, sort / package materials into transport vesicles, cis face (receiving end) and trans face (shipping end) |
| Lysosome (Function, Contains, Originates from…) | Hydrolyze proteins, use enzymes to recycle organelles (autotrophy), come from golgi / ER, pumps H+ ions in / out to activate / deactivate enzymes |
| Nuclear Envelope (Function and Structure) | Encloses nucleus, double membrane (quadrilayer) |
| Nuclear Lamina (Function and Structure) | Maintains nuclear structure, net of proteins |
| Nucleus / Chromatin / Chromosome | Located within nucleus, site of ribosomal RNA, uncondensed DNA, condensed DNA (mitosis, meiosis) |
| Ribosomes (Location. Comparable to…) | Cytosol, ER, Nuclear Envelope, huge enzyme complexes |
| Basic Features of All Cells (4) | plasma membrane (holds thing in, permeable, regulation), cytoplasm (semifluid), genetic material, ribosomes (translation) |
| Prokaryotic Cells (Features) | No nucleus, nucleoid instead, no true organelles, cytoplasm (helps with 99.9% o reactions, require liquid environment) |
| Eukaryotic Cells (Features) | DNA in nucleus, true organelles (allows cell to be larger and compartmentalized), cytoplasm |
| Cell Fractionation and Biochemistry (Enable what?) | Determine functional use of organelles, correlate cell function with structure by studying molecular structure |
| Transmission Electron Microscopes (TEMs, View what?) | See internal details in nm |
| Scanning Electron Microscopes (SEMs, View what?) | Surface details, 3D image |
| Quality of Microscopy (Determines by? Size limit LM) | Magnification (determined by wavelength of light), resolution (clarity), contrast, organelles too small to view in LM |
| Gene (Structure of DA, Directionality, Types of RNA) | Made of DNA, a nucleic acid (AT GC U), RNA (m, t, sn, r) nucleotides account for directionality, DNA is in a double helix, is antiparallel, and made of nucleic acids |
| 7 Functional Groups | Hydroxyl (OH, alcohols), Carbonyl (C=O, in sugars), Carboxyl (COOH, carboxylic acid), Amino (N, amines), Sulfhydryl (S, stabilize protein structures), Phosphate (P, ATP), Methyl (CH3, affect gene expression and hormones) |
| Protein Functions (8) | Enzymatic, Storage (plant seeds), Hormonal (insulin), Contractile (actin and myosin), Defensive (antibodies), Transport (hemoglobin), Receptor, Structural (collagen) |
| Colloid | Stable suspension of fine particles in a liquid |
| Aqueous Solution | Solution where water is the solvent, water can dissolve compounds made of nonionic polar molecules (large proteins) |
| Solute | Substance that is dissolved |
| Solvent | Dissolving agent of a solution |
| Solution | Liquid that is a homogenous mixture of substances |
| Carbohydrates (Many form…, Made of…, Differences, Functions, Structure, Specificity) | Polysaccharide polymers, many form rings, monosaccharides serve as major fuel and raw material for building, differences based on glycosidic linkages on rings forms alpha and beta, enzymes hat digest alpha can't digest beta (hydrolysis) |
| Disaccharide (How is it made?, Process) | Dehydration synthesis joining two monomers |
| Glycosidic Linkages | Covalent bonds of sugars |
| Polysaccharides (Structure, Function Determination, Breakdown Process) | Polymers of sugars, structure / function determined by sugar monomers / position of glycosidic linkages, only certain enzymes can break them down with hydrolysis / enzymes (cellulose) |
| Monosaccharides (Formula Structure, Classification) | Single sugars, multiples of CH2O, classified by location of carbonyl group / confirms ability to use |
| Lipids (Form) | Nonpolar, don't form polymers |
| Fats (Structure, Function, Single, Double) | Made up of glycerol and fatty acids, single bonded are saturated, double bonded are unsaturated fats, nonpolar, hydrophobic, used for energy storage and temperature regulation within the bonds |
| Fatty Acids (Structure) | Long carbon skeleton attached to carboxyl group |
| Steroids (Structure, Polar or Nonpolar?) | Four fused rings of carbon skeletons, nonpolar |
| Phospholipids/ Amphipathic (Function) | Make up cell membranes (90% organisms, arches), amphipathic (polar head, non polar tail) |
| Macromolecule (Bond, Structure, Function) | Large molecules made of thousands of covalently connected atoms, molecular structure / function are inseparable |
| Hydrolysis (Reverse of…, Breaks down…) | Reverse of dehydration synthesis, adds water to break down polymers, used to break down carbohydrates, lipids, and proteins |
| Dehydration Synthesis (How is it sped up?) | Two monomers join together through the loss of water, used to make polypeptide binds for proteins, macromolecule enzymes speed process |
| Polymer | Long molecule made from monomers |
| Surface Tension | Measure of how hard it is to break the surface of a liquid |
| Specific Heat (Water) | AMount of heat that must be absorbed / lost for 1g to change in temperature by 1 degree C, water resists temperature change because of it's high specific heat, minimizes change within limits that permit life |
| Four Properties of Water | Cohesive behavior, ability to moderate temperature, expansion upon freezing, versatility as a solvent |
| Hydrocarbons (Consist of…, Create…) | Organic molecules consisting of only carbon and hydrogen, help create molecular shape |
| Organic Chemistry (Live) | Study of compounds containing carbon, live carbon based with water |
| Carbon Compounds (4) | Proteins, DNA, carbohydrates, lipids |
| Adenosine Triphosphate (ATP, Primary, How does it use phosphate?) | Primary energy- transferring molecule of cell, uses phosphate to change the shape of a bonded molecule |
| Parymadines | TCU |
| Purines | AG |
| Semiconservative Model | Each daughter strand of DNA will have a new strand and an old strand |
| Origins of Replication | Where the two DNA strands separate and create a 'bubble', eukaryotes have hundreds of origins and replications proceeds in both directions because of their linear DNA, prokaryotes have circular DNA and one origin of replication |
| Replication Fork | Y-shaped region where new DNA strands are elongating |
| Helicases | Enzymes that untwist the double helix at the replication fork |
| Single-strand Binding Protein | Stabilizes single-stranded DNA, keeps it open |
| Topoisomerases | Corrects "overwinding" by breaking, swiveling, and rejoining DNA strands |
| Primer | Initial nucleotides in replication, made of RNA, nucleotides can only be added to 3' ends |
| Primase | Enzyme starting RNA chain by adding RNA nucleotides using the old DNA as a template, DNA polymerase recognizes |
| DNA Polymerase | Enzyme that elongates new DNA at replication fork, can elongate at a rate of 500 nucleotides per second |
| Antiparallel Structure | Structure of the DNA double helix, affects replication because one side is the template for the other |
| Leading Strand | Continuous strand adding towards the replication fork |
| Lagging Strand | Strand working away from the replication fork, makes fragments because it does not have a free 3' OH end |
| Okazaki Fragments | DNA segments on the lagging strand |
| DNA Ligase | Joins and latches the segmented pieces together |
| Mismatch Repair | Repair enzymes correct errors in base pairing |
| Nucleotide Excision Repair | A nuclease cuts out and replaces damaged stretches on DNA |
| Telomeres | Nucleotide sequences at the ends of eukaryotic DNA |
| Histones | Proteins responsible for the first level of DNA packing into chromatin, histone tails are highly negatively charged, DNA is also negatively charges, want two negatives so histones slide to allow certain parts to unwind |
| Euchromatin | Loosely packed chromatin |
| Heterochromatin | During interphase, regions of highly condensed chromatin |
| Gene Expression | Process by which DNA directs protein synthesis, linking genes to enzymes |
| Transcription | Synthesis of RNA under direction of the DNA |
| Messaging RNA (mRNA) | Produced by transcription, must go away after use, RNA has half lives |
| Translation | Synthesis of polypeptides under direction of mRNA |
| Ribosomes | Sites of translation, machinery performing translation |
| RNA Processing | Eukaryotic RNA transcripts are modified to yield mRNA, prokaryotes do not have introns or exons |
| Primary Transcript | Initial RNA transcript from any gene |
| Triplet Code | Basis of flow of information from gene to protein, a series of three-nucleotide 'words' |
| Template Stand | One of the two strands of DNA providing template for ordering sequence of nucleotides for RNA transcript |
| Codons | mRNA base tri[plets in translation, read in 5' to 3' direction |
| Reading Frame | Groupings, codons must be read in the correct groupings to produce the correct polypeptide |
| RNA Polymerase | Catalyzes RNA synthesis, pries DNA strands apart and hooks together RNA nucleotides (Uricil instead of thymine) |
| Promoter | Location where RNA polymerase attaches |
| Terminator | Sequencing signaling the end of transcription |
| Transcription Unit | Stretch of DNA that is transcribed |
| Transcription Factors | Mediate the binding of RNA polymerase and the initiation of transcription, DNA binding proteins |
| Transcription Initiation Complex | Completed assembly of transcription factors and RNA polymerase bound to a promoter |
| TATA Box | Promoter, crucial in forming the initiation complex in eukaryotes |
| 5' Cap and Poly-A Tail | Pre-mRNA modification includes adding a cap and tail, they facilitate export of mRNA, they protect mRNA from hydrolytic enzymes, and help ribosomes attach to the 5' end |
| RNA Splicing | Removes introns and joins exons, creating continuous mRNA coding sequence, RNA has enzymatic abilities |
| Spliceosomes | Consists of several proteins and several small snRNP's (ribonucleoproteins) that recognize the place sites, splice out introns |
| Ribozymes | Catalytic RNA that function as enzymes and can splice RNA |
| Alternative RNA Splicing | Some genes can encode for more than one kind of polypeptide, number of proteins an organism can produce is much greater, usually white blood cells or lymphocytes |
| Domains | Modular architecture consisting of discrete regions (alpha-helicies, beta-sheets) |
| Transfer RNA (tRNA) | Translates mRNA into protein, each has anticodon to pair with each codon and an amino acid |
| Aminoacyl- tRNA Synthase | Enzyme matching a tRNA and amino acid |
| Wobble Theory | Flexible pairing at the third base of a codon, allows some tRNAs to bind to more than one codon |
| A-site, P-sire, E-site | A- aminoacyl- tRNA binding site, P- peptidyl binding site, E- exit |
| AUG | Start codon in RNA translation |
| Silent Mutation | No effect on amino acid sequence |
| Base-Pair Substitution | Replacement of a nucleotide and its partner |
| Missense Mutations | Still code for amino acid, but not the right amino acid |
| Nonsense Mutations | Change an amino acid codon into stop codon, leads to a nonfunctional protein |
| Insertions and Deletions | Additions and losses of nucleotide pairs |
| Frameshift Mutation | Insertions or deletions may alter the reading frame |
| Mutagens | Physical to chemical agents that can cause mutations |
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MichaelaMH
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