BIO 110 Test 1 Summary PDF

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BIO 110 Test Study Guide Process of Science  Science is a way of knowing  Who is a scientist? Someone who uses the scientific method  Variables: a. Independent: what you manipulate b. Dependent: what you expect to change during the experiment  Hypothesis? It is possible explanation to the question being asked a. Must be testable b. Must result in quantifiable data  Controls: additional samples done to ensure minimal influence from other variables a. Negative control: sample designed for no effect b. Positive control: sample designed for an effect  Cannot prove your hypothesis  Scientific theory: system of ideas supported by a preponderance (a lot) of data Cells and Macromolecules  Macromolecules a. Carbohydrates b. Lipids c. Proteins d. Nucleic Acids  Eukaryotic Cells are systems that that are composed of 5 functional interacting parts Prokaryotes 1) No Nucleus 2) Single shared compartment  

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Eukaryotes 3) Nucleus 4) Multiple specialized compartments (organelles)

Structure and function are intimately connected Cell Theory a. All living things are composed of one or more cells b. Cells are the smallest living units in an organism c. New cells form from pre-existing cells through the process of mitosis o NO SPONTANEUOUS GENERATION (under the current condition) Why no spontaneous generation? a. In order to create a cell, information to produce all the parts are needed (Genome) b. Need molecules (enzymes, various other resources) to put the information to use c. Need organization of the materials (eg. Need membrane to seal everything in)

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Genome: a set of instructions for producing proteins (work horses) a. Proteins do almost everything in a cell Proteome: set of all proteins in a cell b. Genome produces proteome c. Different cells have different proteome d. Any cell expresses about 10% of possible proteins Building Polymers a. Dehydration reaction: synthesizes a polymer b. Removes water molecule and forms new bond Breaking Down Polymers a. Hydrolysis: breaking down a polymer b. Hydrolysis adds a water molecule breaking a bond Macromolecules of the Cell a. Carbohydrates b. Lipids c. Proteins d. Nucleic Acids Macromolecules are polymers made of sub units joined together

Carbohydrates  Molecule made of C-H-O (1:2:1 ratio) a. Simple sugar (monosaccharide) simplest form  Monosaccharaides can be joined by through dehydration  Glycosidic Bond: covalent bond between sugars b. Disaccharide- 2 c. Oligosaccharide- few d. Polysaccharide- many  Serves as the energy storage molecule (eg. Starch)  Serves as structural molecules (eg. Cellulose) Lipids  Defined by being hydrophobic (water fearing) – nonpolar (wont dissolve in water) a. Not polymers built from sub units b. Structurally diverse c. Triglyceride: energy storage o Glycerol+ 3 fatty acids (hydrocarbon chain)  Fatty acids a. Saturated: no carbon-carbon double bonds o Straight, stack, nicely for solids (fats) b. Unsaturated: at least 1 carbon-carbon double bond o Causes kink (bend at the double bond o Don’t stack nicely together, form liquids (oils)  Phospholipids –structural c. Glycerol+ 2 fatty acids+ phosphate polar group (hydrophilic) d. Amphipathic ( partly hydrophobic and partly hydrophilic)

Cholesterol-hydrophobic a. Component of the cell membrane b. Steroid hormones are built ( to regulate processes) Proteins  Polymers of amino acids  Polymers are linear, and the amino acids are central carbon+ amino group+ carboxyl group  There are 20 amino acids (the same except for different R groups)  Peptide bond: covalent bonds formed through dehydration reaction a. Polypeptide: polymer of amino acids b. N-terminous, c-terminous  Level of protein structure 1) Primary structure: list of amino acids in a polypeptide (n-terminous  c-terminous) 2) Secondary structure: repeated structures within polypeptide  Alpha-helix (spiral)  B-sheet (flat)  Both stabilized by hydrogen bonds 3) Tertiary structure: 3D shape of single polypeptide 4) Quaternary structure: 3D shape of a protein made of more than one polypeptide Nucleic Acids  Polymers made of subunits (nucleotide)  Nucleotides a. 5-carbon sugar (ribose RNA or deoxyribose DNA) b. Nitrogen-containing base (DNA –A, G, C, T) (RNA- A, G, C, U) c. Phosphate group  Nucleic acids are joined by covalent bonds (phosphodiester bond)  Formed by dehydration synthesis  RNA is one strand  DNA is 2 strands joined together by H-bonds (between bases) 

Plasma Membrane  The plasma membrane manages interaction between the outside and inside  Phospholipid bilayer a. Tails: hydrophobic b. Heads: hydrophilic c. Very hard for water to pass through the bilayer (very protective)  Plasma membrane a. Phospholipid bilayer b. Proteins (alpha helix secondary level of proteins)  Fluid mosaic model a. Phospholipids o Lateral movement o Rotation

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o Flexion (fatty acid) o Can’t flip flop b. Proteins o Lateral o Rotate o Drift o Can’t flip flop c. Cholesterol d. Glycolipid (lipid + carbohydrate) e. Glycoprotein (protein + carbohydrate) Factors that affect fluidity 1. Tempurature 2. Nature of the fatty acids in phospholipids o Lots of saturated fats –reduce fluidity o Lots of unsaturated fats- increase fluidity 3. Cholesterol o Moderate temperatures- reduce fluidity Diffusion: net movement of a substance from region of high concentration to region of low concentration  Its not all moving in one direction at once  Equilibrium: equal concentration (net movement is 0) Osmosis: net movement of water across a semi-permeable membrane from area of low solute concentration to an area of high solute concentration.  Concentration gradient: difference in concentration across a membrane  Hypertonic: side of membrane with higher concentration  Hypotonic: lower concentration  Isotonic: same concentration Transport proteins 1. Channel protein: usually allows passage of ions o Aquaporins: water channels 2. Carrier proteins: undergo conformational (shape) change  Movement down the concentration gradient (high  low)  Facilitated diffusion: passive process- no energy required Active transport a. Movement from area of low concentration to an area of high concentration (up the concentration gradient low high) ENERGY NEEDED o Proteins are called pumps (specialized carriers) o Can be linked to source of energy Na+/K+ pump (Sodium/potassium pump) b. 3 Na+ ions out of the cell, 2 K+ into the cell (costs 1 ATP) 1. 3 Na+ from inside bind to the pump ( stimulates transfer of phosphate from ATP to protein 2. Phosphate causes shape change- open to the outside (spits out the Na+)

3. 2 K+ from outside bind o Triggers release of phosphate (pump changes back to original shape) o Spits K+ into the cell  Creating 2 concentration gradients o One for Na+ (high out) o One for K+ (high in)  Creates charge difference across membrane (inside becomes negatively charged)  Electromagnetic gradient: a concentration gradient + a charge gradient o Solute concentration gets lower over time (3 out, 2 in…) o This prevents cells from filling with water (and exploding)  Bulk transport a. Large particles or large amounts b. Substance enclosed in membrane sphere (vesicle)  2 types: o Exocytosis: out of the cell (export of materials) o Endocytosis: into the cell (brings in resources)  Phagocytosis: large solid particles  Pinocytosis: brings in fluid (esp. solutes dissolved in fluid)  Receptor: mediated endocytosis very specific molecules o All very random Functional Organization of Cells o Nucleus o Endomembrane system o Cytosol o Semiautonomous organelles  Nutritional Needs : determined by the volume  Satisfaction of needs: determined by surface area  Animal and plant cells both have mitochondria but only plants have chloroplasts and cell wall  5 Functional system: 1. Plasma membrane 2. Nucleus 3. Endomembrane system 4. Cytosol 5. Semiautonomous organelles  Nucleus o Nuclear lamina  Network of protein fibers  Gives nucleus shape  Helps organize chromosomes

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Endomembrane system o Components  Endoplasmic reticulum (ER): folded membranes adjacent to nucleus  2 types:  Rough ER: ribosomes make it rough (make protein for export)  Smooth ER: makes lipids; detoxification (in the liver)  Golgi apparatus: shipping and receiving (series of membrane sacs)  Receives proteins in vesicles from ER, processes them, ships them to their final destination (ships them in vesicles)  Vesicles  Lysosome: contain hydrolytic enzymes  Autophagy: digestion of defunct organelles Cytosol o Cell makes proteins for itself o Metabolism done here  Cytoskeleton: a set of protein fibers that govern cell shape, movement, positioning, etc. o Networks 1. Microfilaments-polymers of actin protein  Join non covalently  Cell shape, locomotion  Smallest (7nm) 2. Intermediate Filaments  8-10 nm (like cables)  Help cell withstand stress and tension 3. Microtubules  25 nm (hollow tubes)  Separate chromosomes  Organize organelles  Locomotion (some)  Intracellular transport  Centrosome: 2 centrioles (microtubule organizing center) (made of microtubules) Cell junction

1. Tight junctions: waterproof seals between cells 2. Desmosomes: like rivets (very strong) because they are anchored to the intermediate filaments 3. Gap junctions: tunnels that connect cells (communication)  Semiautonomous organelles o Mitochondria, chloroplasts, self governing organelles o Contain their own DNA o Make some of their own protein  Import some proteins from cytosol o Energy transfer Mitotic Cell Division  Purpose of mitosis: 1 parent cell  2 offspring cells (identical to parent)  Big Idea o Cells arise from existing cells through the process of cell division o Chromosome  linear strand of DNA  Cell cycle- series of phases cell goes through as part of a cell division process o G1 (Gap) cell carries out cell functions o S (Synthesis) chromosomes replicate o G2 (Gap) replicate its organelles  1 chromosome = two chromatids

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 the process repeats over and over Prokaryotes have 1 chromosome Eukaryotes have 2-1000 chromosomes Somatic Cells Gametes - Everything that isn’t a gamete (2 sets of chromosomes) Diploid cell (2 sets of chromosomes)

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-Reproductive cells (sperm and egg) Haploid cells (1 set of chromosomes)

Centromere: the region on each sister chromatid where they are most closely attached to each other by proteins that bind to specific DNA sequences. Karyokinesis: 5 stages o Prophase o Prometaphase o Metaphase o Anaphase

o Telophase  G2 of Interphase: o Centrosomes (2 centrioles) o Chromosomes are dispersed (uncondensed)  Prophase o Chromosomes begin to condense o Centrosomes migrate to opposite ends o Begin to form the mitotic spindle  Prometaphase o Nuclear envelope breaks down o Spindle microtubules attach to chromosomes (attach to kinetochores and assemble at the centromere)  Metaphase o Chromosomes reach equilibrium and line up in the center of the cell o Metaphase plate  Anaphase o Centromere divides, chromatids separate (now each chromatid is a chromosome) o Pulled to opposite ends of the cell  Telophase o Chromosomes reach opposite ends o Nuclear envelope reforms  Cytokinesis: o Animal cells  Ring of microfilaments  Pinches cell in 2 o Plant cells  Vesicles form cell plate  Share new cell wall  Cell cycle has a series of checkpoints Energy and metabolism  Big idea: there is energy flow in cells  Types of energy: o Kinetic energy: energy of movement (used to do work) o Potential energy: due to structure or position is energy stored  Energy can be stored within covalent bonds: chemical energy  Energy is released and required

Exergonic Reaction -Energy released > energy required (net

Endergonic reaction -Energy released < energy required (net

release of energy) -Spontaneous (no necessarily quickly)

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input of energy required) -Spontaneous

 Activation energy: brings reactants together  transition state (requirement) (comes from heat) Catalyst: accelerates chemical reaction without being changed itself (lower activation energy)  Biological catalysts: enzymes (most are proteins, some RNA –ribozymes) Substrate: what the enzymes act on  Active site (clef for depression) fits the in substrate  Enzyme reactions are VERY specific (ex. Key and lock) Induced fit: once substrate binds to enzyme, the enzyme undergoes shape change   tighter binding  Puts strain on the bond so it can be more easily broken  Substrate(s)  product(s) Metabolism o Sum of all chemical reactions in an organism o Catabolism: breaking down large molecules into small ones (overall release of energy) o Anabolism: building up larger molecules fro smaller ones (overall requirement of energy input) o Metabolic reactions are often organized into metabolic pathway  Each reaction in the pathway causes small change to substrate  At the end of the pathway  final product  Catalyzed by different enzyme Enzymes need to me regulated 1. Regulate the expression of the genes that encode the enzyme 2. Cellular control- enzymes present but have inactive  Cell receives signal enzyme activated 3. Biochemical regulation: enzyme activity regulated by binding molecule to enzyme Biochemical regulation 1. Competitive inhibition  Inhibitor similar to substrate + binds to active site 2. Noncompetitive inhibition  Regulator molecules binds somewhere other than active site  Inhibitor binds to regulatory site  shape change in enzyme (no longer fits substrate) Feedback inhibition: product of product of a pathway act as inhibitor of first enzyme of pathway  Whole pathway shuts down Allosteric regulation (different shape regulation) Factors affecting enzymes

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1. Temperature: higher temperature, higher activity, BUT above certain temperature, enzymes denature (lose shape) 2. pH 3. Salt concentration- higher salt concentration  partial denotation BIG IDEA  ATP provides the energy to do work and carry out metabolic reactions Energy coupling: coupling an endergonic reaction to the hydrolysis of ATP  Transport work-pumps  Mechanical work- motor proteins

Cellular respiration  Autotrophs: produce their own fuel (self nourishing)  Heterotrophs: consume other organisms to get fuel (outside nourishment)  Mitochondria

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Electrons via NADH

ATP production 1. Substrate level: phosphorylation 2. Oxidative phosphorylation-uses energy from harvested electrons

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Glycolysis (10 reactions-2 phases) 1. Energy investment phase- 2 ATP invested 2. Energy recoupment phase (pay off)-4 ATP produced (electrons harvested)  2 ATPs used to rearrange glucose so it can be split into 2-3C  split into 2-3C (one G3P and other converted to G3P)  important products:  reduced NADH +H+  2 pyruvates Pyruvate oxidation o One carbon cleaved off  CO2  Replaced by CoA o Electrons harvested  (NADH+ H+) 2 o Product: Acetyl CoA (x2) Citric Acid Cycle (takes place in matrix) (8 reactions -2 parts) 1. Priming-preparing Acetyl CoA to have electrons extracted (2 reactions) Acetyl CoA +4 Carbon molecules  6 Carbon molecules 2. Energy extraction: electrons harvested in 4/6 reactions. ATP is produced Oxidative phosphorylation 1. Electron transport o Electron transport chain: series of multi protein complexes in inner mitochondria membrane o Electron carriers hand electrons to ETC o Energy of electrons siphoned off gradually  work  ETC complexes use electron energy to pump protons from matrix  inter membrane space  Create an electrochemical gradient of protons  Proton motive force : drives protons to want to move back to matrix  Electrons handed off to oxygen (combines with 2 protons =H2O) ATP synthase o As protons move in through ATP synthase, causes rotor portion to turn

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 As rotor turns, causes conformational change in enzyme part  Joins ADP to P ATP o For each NADH+H+ about 2.5 ATPx10= 25 ATP o For each FADH2  about 1.5 ATPx2=3 ATP o A total of abot 30-32 ATP produced (per glucose) Fermentation o Recycles NAD+ under low oxygen conditions so glycolysis can produce more ATP...