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[VERSION 2] GENERAL BIOLOGY I Study Guide for Test 1

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Department
Biological Sciences
Course
01:119:115
Professor
A L L
Semester
Fall

Description
Biology Exam 1 Study Guide Types of reactions • Exergonic: spontaneous; free E decreases; E released • Endergonic: • Synthesis/Anabolic: put together • Decomposition/Catabolic: take apart Powerpoint 1 Characteristics of Life 1. Cells and organization a. Organisms maintain internal order b. Simplest organism is cell 2. Energy use and metabolism a. Need energy to do anything b. Energy used in chemical reactions is metabolism 3. Response to environment a. Organisms respond to environmental changes b. Ex: phototaxis 4. Regulation and homeostasis a. Organisms regulate bodies to maintain stable internal conditions b. Known as homeostasis 5. Growth and development a. Organisms grow, producing larger cells b. Develop defined characteristics 6. Reproduction a. Organisms must reproduce to survive b. Transmit genetic material 7. Biological evolution a. Traits that promote reproductive success and promote survival b. Populations evolve, not individual organisms 8. Structure determines function a. Multiple levels of organization b. Ex: webbed vs. non-webbed feet for swimming vs. walking c. Ex: cells with lots of villi = more absorption Levels of Organization (red indicates focus of lesson) 1. Atoms 2. Molecules and macromolecules 3. Cells 4. Tissues 5. Organs 6. Organism 7. Population 8. Community 9. Ecosystem 10. Biosphere Evolutionary History • Life on earth began as primitive cells 3.5 to 4 billion years ago (bya) • Cells went through evolutionary changes to create today’s species • Evolutionary history helps us understand structure and function of organisms Mechanisms of evolutionary change 1. Vertical descent with modification a. Progression of changes in a lineage b. New species evolve from pre-existing species by the accumulation of mutations c. Natural selection takes advantage of beneficial mutations d. Evolutionary change involves modifications of pre-existing characteristics e. Structures may be modified to serve new purposes f. Ex: Walking limbs were modified*** into a dolphin’s flipper or a bat’s wing 2. Horizontal gene transfer a. Genetic exchange between different species (usually prokaryote) b. Relatively rare Tree/Web of life Tree of life: focuses on vertical evolution Web of life: includes horizontal gene transfer Taxonomy: grouping of species based on common ancestry Domains: • Bacteria: unicellular prokaryote • Archaea: unicellular prokaryote; often living in extreme environments • Eukarya: unicellular AND multicellular eukaryotes o Complex cells with nucleus o Kingdoms:  Protista  Plantae  Fungi  Animalia Ex: Clownfish (LOOK UP EXAMPLE IN POWERPOINT) Binomial nomenclature: genus, species Genome: the complete genetic makeup of an organism; carries info to make proteome Genomics: techniques used to analyze DNA sequences in genomes Proteome: the complete protein makeup of an organism Proteomics: techniques used to analyze the proteome of a single species and the comparison of proteomes of different species Ex: crystal jellyfish (Aequorea Victoria) is bioluminescent; makes GFP, which is only expressed in proteome of some cells (indicated by glowing spots); Nobel Prize to Martin Chalfie, Roger Tsien and Osamu Shimomura Biology as a scientific discipline: Science: the observation, identification, experimental investigation, and theoretical explanation of natural phenomena Scientific method is used to test theories Scientists also gather information Different branches of biology study life at different levels using a variety of tools. Ecology, anatomy, physiology, cell biology, molecular biology, etc. As new tools become available, they allow scientists to ask new questions Systems biology aims to understand how emergent properties arise, at any level Cell biology and ecology Ex: cell biologist use microscope to see cell function; ecologists study species in native environments Hypothesis: proposed explanation for a natural phenomenon; proposition based on previous observations or experimental studies; predictions that can shown to be correct or incorrect; useful hypotheses are testable; can be supported/rejected based on more observation; never really proven Theory: Broad explanation of some aspect of the natural world that is substantiated by a large body of evidence; allows us to make many predictions; never really proven Understanding Biology: curiosity is key; no rigid steps 1. Discovery-based science: Collection and analysis of data without the need for a preconceived hypothesis a. Goal: gather information b. leads to hypothesis testing if successful c. Ex: cystic fibrosis i. 1945, Dorothy Anderson determined it was genetic disorder ii. Later, the CF gene was identified that regulates transport of Cl- ions 2. Hypothesis testing a. Five stages i. Observations are made regarding natural phenomena. ii. These observations lead to a testable hypothesis that tries to explain the phenomena. iii. Experiments are conducted to determine if the predictions are correct. iv. The data are analyzed. v. The hypothesis is accepted or rejected. 3. Common features: data collection and analysis Science as a social discipline: 1. Peer review 2. Conferences 3. Mentoring young scientists 4. Talk to the public 5. Outreach Powerpoint 2 4 main elements of life: CHON Hydrophilic, hydrophobic, amphipathic Water properties: • Participates in chemical reactions (hydrolysis or condensation) • Provides force or support • Evaporative cooling • Cohesion and adhesion; capillary action • Surface tension • Lubrication • Dissolve salts • Solvent o Can dissolve other chemicals o Polar (hydrophilic) = soluble o Non-polar (hydrophobic) = insoluble • Adhesion • Chemical reactivity (removed and added to break up or build compounds) • Thermal stability Isomers • Structural isomers • Stereoisomers o Cis-trans isomers  Cis: symmetrical  Trans: x-axis translatable o Enantiomers (mirror image) Reactions: 1. Decomposition – catabolic o Hydrolysis: splitting a polymer’s covalent bond by water 2. Synthesis – anabolic o Dehydration synthesis: monomers covalently bond together to form a polymer; remove water 3. Exchange: part synthesis and part decomposition 4. Reversible Macromolecules 1. Carbohydrates: CHO; C (HnO)2 n a. Monosaccharide b. Glucose + Fructose  (glycosidic bond) sucrose + water c. Polysaccharides i. Energy storage: starch, glycogen ii. Structural: cellulose, chitin, glycosaminoglycans 2. Lipids a. Nonpolar b. Fats, phospholipids, steroids, waxes c. Uses: energy storage, membranes, steroids/hormones/vitamins, insulation, protection d. Ex: Saturated: stearic; unsaturated: linoleic e. Triglycerides: glycerol + 3 fatty acids  (ester bond) triglyceride f. Phospholipids: glycerol + 2 fatty acids + phosphate group i. Amphipathic: polar heads, nonpolar tails g. Steroids: four interconnected rings of C i. Usually insoluble ii. Ex: cholesterol iii. Differences in structure = specific biological properties 1. Ex: estrogen vs. testosterone 3. Proteins: determine structure and function: CHON (and trace, like sulfur) a. Amino acid: 20 types b. Have functional groups (aka variable sidechain) that determine structure and function c. Amino acid + amino acid  (peptide bond) polypeptide d. Protein structure: i. Primary 1. Amino acid sequence 2. Encoded directly by genes 3. Chaperone proteins help keep amino acids separated until ready to fold ii. Secondary: protein folding 1. α-helix 2. β-pleated sheet 3. Random coiled regions iii. Tertiary: complex 3D shape iv. Quaternary: made of 2+ polypeptides (monomeric/multimeric) 1. Individual polypeptide chains are protein subunits e. Protein folding (in red are four factors with which protein-protein interactions occur): i. Hydrogen bonds: between atoms in polypeptide backbone and between different side chains ii. Ionic bonds and other polar interactions: between oppositely charge side chains iii. Hydrophobic effects: nonpolar amino acids in center of protein avoid water iv. Van der Waals forces: between close atoms v. Disulfide bridges: covalent bond between 2 cysteine side chains 4. Nucleic Acids: storage, expression, and transmission of genetic information a. Proteins: maintain structure/shape, communication, transport, identification, movement, calalyst b. DNA: Stores genetic information encoded in the sequence of nucleotide monomers c. RNA: Decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain d. Nucleotide monomer: made of phosphate group, 5C sugar, nitrogenous base i. ATP: energy carrying molecule ii. cAMP: activates metabolic pathways iii. Incorporated into DNA and RNA Cell theory 1. All living organisms are composed of one or more cells 2. Cells are the smallest units of life 3. New cells come only from pre-existing cells by cell division Cell size • Human cell: most 10-15 µm o Egg cells: 100 µm o Nerve cell: 1 meter long • SA:V ratio Microscopy • Magnification: ratio between the size of an image produced by a microscope and its actual size • Resolution: ability observe two adjacent objects as distinct from one another • Contrast: how different one structure looks from another (dyes help) • Types: o Brightfield/Light: dark objects are visible against a bright background o Phase contrast: improved contrast of denser structure Cell structure • Prokaryotes: simple, no nucleus o Bacteria: 1 µm – 10 µm; abundant  Plasma membrane: • Cytoplasm • Nucleoid region – DNA • Ribosomes – Proteins  Outside plasma membrane: • Cell wall – support/protection • Glycocalyx – protection/evasion of immune system • Appendages (pili, flagella) – attachment/movement o Archaea: 1 µm – 10 µm; less common; extremophiles • Eukaryotes: complex, DNA within membrane-bound nucleus, internal membranes form organelles o Animal cell (GO BACK AND LOOK AT PICTURES) o Plant cell (GO BACK AND LOOK AT PICTURES) o Be able to compare plant and animal cells  Central vacuole; chloroplast; cell wall Powerpoint 3 Cells: even though DNA is identical, cells in same organism have different proteomes so that organism can produce different types of cells Plasma membrane • Function: membrane transport; cell signaling; cell adhesion • 3 macromolecules: protein, lipid, carbohydrate • Two leaflets (halves of bilayer) are asymmetrical • Lipids can rotate/move laterally • Flip-flop of lipids from one side to another requires flippase + ATP • Lipid rafts o A group of lipids floats together as a unit within the larger body of lipids in the membrane o Composition of lipid raft is different than rest of membrane  High concentration of cholesterol  Unique set of transmembrane and peripheral proteins  Cell Signaling • Proteins: o Peripheral: stay near membrane; not embedded o Integral: embedded  Transmembrane: Region(s) are physically embedded in the hydrophobic portion of the phospholipid bilayer  Lipid-anchored: An amino acid of the protein is covalently attached to a lipid  Functions: act as channel for ions/hormones, can identify cell, transmit outside signals to inside (can help with cell reproduction)  Functions from ppt: • Receptors • Enzymes • channel proteins (gates), • cell-identity markers, • cell-adhesion molecules • What contributes to fluidity? o More unsaturated fatty acid tails in phospholipids = increased fluidity (less tightly packed) o To a point, more cholesterol will increase space between molecules and increase fluidity. Too much cholesterol will make the membrane TOO rigid. • MEMBRANE FLUIDITY WILL BE QUIZ SHORT ANSWER ON THIS: • A group of phospholipids with saturated fatty acyl tails will be able to be more tightly packed and will ultimately make a cell membrane LESS fluid. In class, I said that unsaturated fatty acids in phospholipids will make membranes less fluid. While an individuaphospholipid may be less motile (moving laterally or spinning) if it has an unsaturated fatty acyl tail, it will increase the space between phospholipids and this increase space translates into increased membrane fluidity. • A note about choles... cholesterol is a little tricky. It's very rigid and will impede the local movement of phospholipids, but its presence will increase the space between phospholipids thereby increasing membrane fluidity. • What's also tricky is that cholesterol-containing membranes are more fluid in lower temperatures (it prevents cracking of the membrane) and less fluid at higher temperatures like physiological mammalian temperatures. This may seem contradictory to the above note, but the distinction is what is being compared to what. • In a mammalian cell, cholesterol is stabilizing and gives some structure to the membrane. Increasingly more cholesterol, *to a point*, will increase membrane fluidity, but too much cholesterol will have the opposite effect and decrease the fluidity. Cytosol: region of eukaryotic cell that is outside organelles but inside plasma membrane • Metabolism is coordinated within cytosol
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