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Biology 107
"glossary"
| Term | Definition |
|---|---|
| Water | -universal solvent -polar -dipoles (allows for favorable interactions with other polar molecules) -high electronegativity |
| Covalent bonds | -sharing of electrons in bonds -strong bond type |
| Ionic bonds | -electron from one atom is fully associated with the other atom in the bond -strong bond type |
| Hydrogen bonds | - dipole-dipole interactions (crucial in life) -weak bond type |
| Van der waals interactions | -transient interaction of charges -very weak bond type |
| Organic molecules | -contain H & C bonds -C is the backbone of organic molecules -C is weakly electronegative |
| Carbon | -can bond to four other atoms -can form C-C chains -can form double and triple bonds with other C |
| Monomer | -single building block of polymers |
| Polymer | -form all macromolecules important to life |
| Dehydration synthesis (Condensation reaction) | -adds monomers into polymer chains by catalyzing covalent bonds -water is a biproduct -requires energy |
| Hydrolysis | -adds water to break a polymer chain -releases energy |
| Carbohydrates | -Function: energy storage, cell structure, cell to cell recognition -Monomer (monosaccharides): have a C chain 3-7 C long, can be linear or ring shaped -Ex. Glucose (mono) and Sucrose (di) -glycosidic bonds |
| Polysaccharides | - Starch (energy storage), glycogen (energy storage), cellulose (structure of cell wall), Chitin (structure) |
| Lipids (fats) | - hydrophobic (nonpolar) -Fatty acids -> single chains of HC ending w/ COOH -16-18 C long -can attach to a 3C glycerol |
| Fats (triglycerides) | -energy storage for animals -Can be saturated (straight tails) or unsaturated (kink in tails) |
| Phospholipids | -Structural component of membranes -2 HC chains attached to a glycerol backbone via ester linkages with a phosphate group attached to the 3rd C of glycerol -amphipathic (both hydrophobic and philic ends) |
| Steroids (lipid-based cholesterol) | -Function: Hormones (testosterone), major component of cell membrane in animals, modulate membrane fluidity, increases membrane stiffness |
| Proteins (polymer of a.a) | -involved in every biological task -20 biological relevant a.a, (R-group) -directionality N-->C |
| *R-group | 1)nonpolar -> R = HC 2)polar uncharged -> R group contains OH or SH 3) polar charged acidic -> R group contains COO- 4)polar charged basic ->R group contains NH2+ |
| Structure of Proteins | 1°-polymerization of a.a. (peptide bond) 2°- protein folding in alpha helix or beta pleated sheets 3°- 3D folding, hydrophobic R groups aggregate to the middle away from water which drives the folding 4°- globular units of multiple protein chains |
| Chaperones | -proteins that assist in folding other proteins -proper folding is essential for proper function -if misfolded, they are degraded |
| Nucleic Acids (DNA/RNA) | -Function: store and transmit hereditary info |
| DNA (molecule of heredity) | - polymer of nucleotides - contains all info essential for life -transmits info between cell generations |
| RNA (transmits info with cell) | -polymer of ribonucleotides -many functions: info transmission (mRNA), translation (tRNA & rRNA), regulation (siRNA & miRNA), splicing (snRNA) |
| Structure of ntd polymer | -SC sugar=ribose, nitrogenous base, phosphate group -Pyrimidines-> cytosine, thymine, uracil (only RNA) -Purines -> guanine, adenine -Pyrimidine pairs with purine |
| Micelle | -Conical -one tail -forms a circle with other phospholipids |
| Bilayer | -Cylindrical -two tails |
| Phospholipid within bilayer | -mobile (lateral movement common, flip flop rare) -flip flop movement facilitated by enzyme called flippine |
| Passive Transport | -movement from high to low concentration -permeable substances only -osmosis |
| -tonic solutions | -hypotonic-> water moves into cell (solute out), cell swells in mammals, doesn't in plants bc cell wall -isotonic-> no net movement of water -hypertonic->water moves out of cell (solute in), cell shrivels (plants = plasmolysis) |
| Facilitated diffusion | - down concentration gradient -two types: channel & carrier proteins -impermeable substances need integral membrane protein to cross bilayer |
| Channel protein | -integral membrane protein with a specific pore to allow passage of a solute |
| Carrier protein | -integral membrane proteins that transport a solute using a conformational change -SPECIFIC -can be gated (open and close in response to stimulus) -highly regulated |
| Active Transport | -Transport molecules up concentration gradient w/ energy -Used to: concentrate nutrients, expel waste, maintain electrochemical gradient -Ex. sodium/potassium pump -> maintains a charge difference across the membrane |
| Cotransport | -transport of 2 molecules using the same transporter |
| Bulk transport | - molecules too big to pass thru a transport protein must use a bulk transport mechanism -involves formation of vesicles -Exocytosis (out of cell), endocytosis (into cell), receptor mediated (carries specific molecules according to receptor) |
| Prokaryote | -small -bacteria |
| Bacterial cell structure | -DNA (circular genome), fimbrae (for attachment), cell wall & membrane, ribosomes, flagella (for movement) -NO membrane-bound organelles -BUT preforms all fxns eukaryotes can |
| Bacterial flagellum | hook-> rotation about the hook allows movement filament- >composed of quaternary structure of flagellin -basil apparatus-> anchors filament to membrane = contains a gear system that allows rotation |
| Bacterial cell wall | -Gram positive-> thick layer of peptidoglycan (PG), PG is a structural polysaccharide -Gram negative-> thin layer of PG surrounded by a lipopolysaccharide layer |
| Antibiotics | -Function: kills bacteria pathogens by targeting bacterial specific structures-> bacterial cell wall and ribosomes |
| Microbiome | -collection of micro-organization found in any given habitat |
| Eukaryotic cell structure | -flagellum, microtubule organizing system, nucleus, nucleolus, rough & smooth ER, Golgi, mitochondria (mito), |
| Endomembrane system | -Nucleus, nucleolus, nuclear envelope, ER, Golgi, lysosomes, vacuoles. |
| The nucleus | -Function: most of the cell's DNA is stored in the nucleus arranged as linear chromosomes, chromatin packing (formation of chromosomes) |
| Nucleolus | -Function: site for rRNA transcription and ribosomal subunit assembly |
| Nuclear envelope | -Function: separates nucleoplasm from cytoplasm - double membrane bound -2 phospholipid bilayers (outer membrane is continuous to ER) |
| histone | -positively charged protein used in chromatin packing - |
| Endoplasmic Reticulum (ER) | -Rough ER: fxn-> site of protein translation & protein quality control. translation of proteins (called bound ribosomes) destined for the endomembrane system Smooth ER: fxn-> ion storage, phospholipid & steroid synthesis, detoxification of drugs/alchol |
| Golgi apparatus ("FedEx" of cell) | -Structure: cisternae (flattened membrane bound faces), Cis, medial (modifies & sorts cargo), & trans faces -Golgi trafficking: vesicle trafficking (cargo moves thru from cis->medial->trans), cisternal maturation (MOST LIKELY, cis becomes medial etc) |
| Lysosomes (cell stomach) | -digestion of macromolecules from phagocytosis -contains hydrolytic enzymes -pumps H+ into compartment -kept at low pH to avoid autophagy (self-eating) |
| Vacuoles | -Fxn depends on cell type: food, contractile (pump out excess water), & central vacuole (specific to plants, storage & part of endomembrane system) |
| Plant cell wall | -Fxn: maintains cell shape and prevents excess uptake of water and prevents osmotic lysis structure: main ingredient is cellulose |
| Stomata | Openings that allow rapid exchange of nutrients and gases |
| Animal extracellular matrix (ECM) | Fxn: maintains cell attachments across long distances, allows communication, maintains tissue integrity, stores growth factors Structure: secreted glycoproteins (collegen, fibronectin, integrin) |
| Collegen | Forms the matrix of the ECM and connects cells over long distances |
| Fibronectin | Links collegen to integrins |
| Integrins | Proteins that link the ECM and MF |
| Epithelial cells | -must stay connected to the ECM, if disconnected then commits cell suicide (apoptosis) Epithelial layers: layers of cells between you and environment (skin) |
| Cancer connection | -90% of cancer occurs in the epithelium -epithelial cells are vulnerable to b/c exposed to carcinogens -major early step is loss of attachment to the ECM and failure to commit apoptosis |
| Animal cell-cell attachments | -set of intercellular junctions in epithelial cells Fxn: maintain tissue integrity -three attachment types (Gap & tight junctions, desmosomes) |
| Tight junctions | Fxn: act as rivets to seal cells together and prevent passage of molecules btwn cells and environment |
| Desmosomes | Fxn: distribute stretching force across tissue and connect to adjacent cells exoskeleton via intermediate filaments |
| Gap junctions | Fxn: provide non-selective transport of small molecules between adjacent cells and allows sharing and cell signaling (gap jxns in heart muscles allow for the spread of calcium btwn cells to signal contracting) |
| Metabolism | -The totality of an organism's chemical rxns, managing the materials and energy resources of the cell -All of cells chemical rxns |
| Anabolism | -Rxns that require energy to build the cell -linked w/ catabolism via ATP |
| Catabolism | -Rxns that release energy from nutrient breakdown -linked w/ anabolism via ATP |
| Thermodynamics | -The study of energy transformation/conversion |
| First law of Thermodynamics | -Energy cannot be created nor destroyed |
| Second law of Thermodynamics | -The energy of the universe is always increasing |
| Entropy | -Measure of randomness/disorder of a system -heat is the most disordered form of energy -A rxn is spontaneous if the disorder of the universe increases out, then you can increase the order of the system |
| Free Energy | -G (free energy) = H (total energy of a system) - T (temp) * ΔS (entropy) -High free energy = organized & low entropy -Low free energy = disordered & high entropy -Negative ΔG are spontaneous = exergonic --Positive ΔG are non-spontaneous = endergonic |
| Energy coupling | -Energy from exergonic rxns are used to power endergonic rxns -can be direct coupling by coupled transport w/ the release of Na+ -Can be indirect w/ ATP |
| ATP (Adenosine Triphosphate) | -The cellular energy currency -Bonds that join the three phosphates onto adenosine are high energy bonds and store energy -Hydrolysis of these bonds release energy = exergonic (ΔG = -13 kcal/mol) -Contains PE due to position and composition |
| Enzymes (-ase) | -Biological catalysts that provide an alternate energy path for a rxn to proceed -Rxn in both endergonic and exergonic rxns -HIGHLY regulated |
| Autotroph | "self-feeders" -Use inorganic CO2 as C source, fix to organic C (highly endergonic) -Photoautrophs = use light energy to power fixation -Chemoautotrophs = use redox rxn energy to power C fixation (only bacteria) |
| Heterotroph | -Use organic C as C & energy source -Chemoheterotrophs = use organic C as main nutrients -Photoheterotrophs = use light energy & organic C (bacteria) |
| Chloroplast | -Site of photosynthesis -double membrane bound with stacks of internal membrane called thylakoids -Stroma = site of the calvin cycle -Thylakoid lumen = site of light rxns |
| Photosynthesis | (6 CO2 + 6 H2O + light -> C6H12O6 + O2) -O2 is waste -CO2 is reduced to glucose |
| Light reactions | Use energy carried by light & convert it into chemical energy in the form of ATP & NADPH which are used to drive the calvin cycle |
| Light absorbed | -Absorbed by pigments -absorbed energy is usually released as heat or fluorescence (unless energy is converted) -Photosystems capture light energy & convert it to chemical energy |
| The Photosytems | -contain pigments such as chlorophyll (main), xanthophylls, carotenoids, etc. -absorbed light excites e- and moves them through the photosystems |
| Electron transport chain (ETC) photosynthesis | -A set of increasing strength e- acceptors -allows energy from excited e- to be converted into a H+ chain releasing energy |
| Energy conservation of Photosynthesis | Photosystems (1) = convert light energy into chemical energy in the form of an excited e- ETC (2&3) = 2) excited e- passes through an ETC & releases energy via redox rxns used to pump H+ and create a gradient. 3) excited e- from P(i) used to reduce NADP+ |
| Chemiosmosis | -Formation of ATP using H+ gradient & ATP synthase -Respiration = oxidative phosphorylation Photosynthesis = photophosphorylation |
| ATP synthase | An enzyme complex that couples an endergonic rxn (ADP + P(i)-> ATP) with an exergonic process (dissipation of H+ gradient) |
| Calvin cycle | POINT: to fix C by the conversion of atmospheric to organic (highly endergonic) -three phases: Carbon fixation, Reduction, and Regeneration |
| Carbon fixation | One CO2 molecule per turn of cycle. Turn cycle 3 times to produce one G3P w/ the enzyme Rubisco |
| Reduction | The NADPH from light reactions is used to reduce fixed C (NADPH donates e-) |
| Regeneration | RuBp inhibits Rubisco to regulate carbon fixation |
| Cyclic Electron flow | -If ATP is low in chloroplast, excited e- goes back to ETC to be pumped through and create ATP w/o NADPH |
| Respiration | -Catabolic (energy releasing) -POINT: Complete oxidation of glucose & convert to energy -Three phases: Glycolysis, Krebs cycle, ETC -Occurs in mito -pyruvate "decides" to enter the mito to complete respiration (controlled by the availability of O2) |
| Glycolysis | -The conversion of glucose to pyruvate -POINT: to begin the oxidation of glucose |
| Transition reaction | -oxidation of pyruvic acid to Acetyl CoA when pyruvate enters the mitochondria -catalyzed by pyruvate dehydrogenase (PDH) |
| Krebs cycle (TCA/Citric Acid cycle) | -POINT: complete oxidation of glucose -O2 released, occurs in matrix of mitochondria, 2 ATP produced by SLP |
| ETC (respiration) | -Across the MIM -e- from NADH or FADH2 are used in redox rxns to power H+ pumping. FADH2 donates e- at a lower energy level (complex II) |
| Fermentation | -POINT: recycle NAD+ for continued glycolysis in eukaryotes -Pyruvate is reduced to waste & acts as an e- acceptor -2 pathways: Lactic acid and Ethanolic |
| Ethanolic Fermentation | -when oxygen is NOT available, some cells have the capacity to undergo fermentation |
| Cell division (mitosis) | Key roles: Reproduction: unicellular organisms divide to produce offspring Development: Multicellular eukaryotes are composed of many cells which arose by mitosis of a single fertilized egg |
| Prokaryote cell division (binary fission) | -Simpler than mitosis (only one chromosome) -creates 2 genetically identical daughter cells |
| Prokaryotic growth curve | 1) Lag phase: cells growing but not dividing 2) Log phase: all cells are dividing 3) Stationary phase: cell death, nutrients and space become limiting 4) Death phase: death>division due to accumulation of wastes and depletion of nutrients |
| Eukaryotic cell division | -Multiple linear chromosomes inside a nucleus -creates 2 genetically identical daughter cells |
| Chromosome | -one copy of genetic info, chromatid product of DNA replication. -Chromatids attach in a chromosome at a centromere -Kinetochore = protein complex that assemble at the centromere |
| Cell cycle | 4 distinct phases: -G1: normal cell activities, cell is "deciding" to divide -S: Synthesis phase (DNA replication) -G2: normal cell activities, cell preparing to divide (2x DNA) -M: Mitosis, separation of chromatids |
| Mitosis | -unique cell cycle phase where the DNA is equally separated into daughter cells -6 phases: prophase, prometaphase, metaphase, anaphase, telophase, cytokinesis |
| Prophase | -MAIN PROCESS: Chromosomal condensation, packaging of chromosomes into fully condensed mitotic chromosomes -cell with 2 chromosomes -Microtubules (MT) are responsible for moving chromosomes around cell |
| Prometaphase | -MAIN PROCESS: nuclear envelope break down (NEBD), MT polymerization invades nuclear area to attach to kinetochore or centromere -MT grow and shrink until they contact a kinetochore (fishing) |
| Metaphase | -MAIN PROCESS: line up chromosomes at metaphase plate/division plane -Chromosomes are moved by pol/depol of MT (primary force) |
| Anaphase | -MAIN PROCESS: separation of sister chromatids (each molecule of DNA is now called a chromosome) -Kinetochore MT pull chromosomes to pole by depol dynein |
| Telophase | -MAIN PROCESS: nuclear envelope reformation, chromosomal decondensation. |
| Cytokinesis | -MAIN PROCESS: separation of cytoplasm -Actin filaments bundle a cytokinetic ring and myosin constricts it -eventually the contractile ring separates cytoplasm into 2 daughter cells |
| Cell cycle control | 3 checkpoints -> decision points to decide when a cell should divide -Restriction (G1) checkpoint, G2 check point, Metaphase checkpoint. If cell passes the requirements cell division continues |
| Cancer | -uncontrolled cell division, ~90% of all cancers are epithelial in origin -cancers are accumulations of random mutations that cause uncontrolled cell division -ignore restriction checkpoints |
| DNA | -carries genetic information -double helix -complementary base pairing (A-T, C-G) -antiparallel (5'-3', 3'-5') -purine pairs with pyrimidine |
| Griffiths Transformation experiment | -Asked "is there a transforming principle?" -proved the existence of a transforming principle (an abiotic factor that carries hereditary info) |
| Avery, Macleod and McCarty experiment | -Asked "what is the transforming principle?" -concluded that DNA was the transforming principle |
| Hershey and Chase (phage-in-a-blender) experiment | -Asked "is DNA the universal transforming principle?" -used radioactive material to detect if the DNA or protein entered the bacteria -concluded that DNA is the universal transforming principle |
| Chemical composition of DNA | -sugar-phosphate backbone -phosphodiester bonds -H bonds between bases (provides specificity) -Base stacking = hydrophobic <- main stabilizing force of double helix |
| DNA replication | -Semi-conservative replication: products of replication are composed of one daughter strand and one parent strand -Daughter strands are complementary copies of parent template |
| Meselson-Stahl experiment | -wanted to determine which hypothetical process of DNA replication was correct (conservative, semi-conservative, or dispersive) -concluded that semi-conservative replication was the correct model |
| Helicase | unwinds parental double helix at replication fork |
| Single-strand binding protein | Binds to and stabilizes single-stranded DNA until it can be used as a template |
| Primase | Synthesizes an RNA primer at 5' end of leading strand and of each Okazaki fragment of lagging strand |
| DNA pol III | Using parental DNA as a template, synthesizes new DNA strand by covalently adding ntds to the 3' end of a pre-existing DNA strand or RNA primer |
| DNA pol I | Removes RNA ntds of primer from 5' end and replaces them with DNA ntds |
| DNA ligase | Joins the 3' end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand |
| Flow of information | DNA (store info) --transcription(trxn)--> mRNA (info transmission) --translation--> protein (info use) |
| Gene (general) | -Stretches of DNA that contain hereditary info (unit of heredity) -all genes must have a promoter (site of RNA pol assembly) -Promoter = sequence of DNA that transcription factors bind to -multiple genes in chromosome |
| Transcription | -occurs 5' to 3' (DNA read 3' to 5') - uses template strand, coding strand not used -Transcript = RNA product -enzyme of transcription is RNA polymerase |
| Prokaryotic gene | -Conserved elements that direct gene expression (TATA box) -TATA box = rich AT sequence found before transcription starts -Transcription factors (TFs): proteins that can read DNA at TATA box (recruits RNA polymerase) |
| Eukaryotic gene | -Lots of different DNA elements that regulate transcription (combinatorial control) -has enhancer elements (DNA) that activator protein binds to -initiation complex involves multi-subunit looping of DNA to enhance RNA polymerase binding |
| Translation | The process in which genetic code carried by mRNA directs the synthesis of proteins to amino acids |
| Exons | amino acid encoding regions which contain expressed sequences found in both a gene's DNA and mature mRNA (coding) |
| Introns | non-amino acid encoding regions which contain intervening sequences found in a gene's DNA but not in the mature mRNA (non-coding) |
| tRNA | adapter molecules that mediate the transfer of information from nucleic acids to proteins antiparallel & complementary base pairs w/ codon in mRNA. can recognize more than one codon for the a a they carry. two regions: a a folding & mRNA binding region |
| Aminoacyl tRNA synthetase (the translator) | -Correct matching of tRNA and its associated a. a. -20 different synthetases for the 20 different a. a. -fxn: pairs the a. a. to tRNA based on anticodon sequences |
| Ribosomes | -catalyze peptide bonds -Facilitate the specific coupling of tRNA codons during protein synth -Two major subunits: large ribosomal subunit, small ribosomal subunit and its assoc rRNA -large contains 3 sites: A= approach p= Polymerization & E = exit |
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ldquinn
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