Study Guide for Final Exam - Principles of Biology | BIOL 1105, Study notes of Biology

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Biology Final Study Guide Properties of Life: 1) cellular organization—complex assemblages 2) sensitively—respond to stimuli 3) growth—metabolism 4) development—gene-directed changes 5) reproduction—passing on genes 6) regulation—coordinating internal processes 7) Homeostasis—maintaining constant internal conditions 8) heredity—possess a genetic system consisting of DNA; allows evolution over time Deductive: general  specific Inductive: specific  general Reductionism: to study small parts in a system Organic Compounds (CHON) Theory: proposed explanation, body of concepts NOBLE GASES: He,Ne,Ar, Kr,Xe,Rn ==nonreactive LEOGER: Loss of electrons is oxidation, gain of electrons is reduction Covalent Bonds (sharing)----Ionic Bond(attraction of opposite charges)-----Hydrogen Bond(sharing of H atoms)----Hyrdrophobic (forcing hydrophobic near polar side)----Van Attraction(weak attractions due to opposite polar clouds) WHEN H bonds break=absorb heat WHEN H bonds form=release heat Chemical Reactions changed by: TEMPERATURE, CONCENTRATION OF PROD/REACT., & CATALYSTS ACIDS: the stronger it is, the more H+ ions it produces and the lower its pH BASES: lowers the H= ions, the pH values are above 7 Solution consists of solute which is dissolved in solvent (what is dissolved) Carbohydrates: starch & glycogen (energy storage), cellulose(plant cell wall), chitin(structural support) Lipids: used for fuel, energy, metabolic, water, sex attractant Functional Groups: Amino(proteins), Hydroxyl(Alcohols), Carboxyl(organic acids), Sulfhydryl(between cysteines), Phosphate(nucleic acids), Methyl(proteins), Carbonyl(carbohydrates, nucleic acids) Nucleotide: Nitrogenous base, Phosphate Group, 5-Carbon sugar Triglycerides consist of fatty acids and alcohol MONOSACCHARIDES:5-Carbon sugars:ribose, deoxyribose Dissociation can change back, but denaturation cannot 6-Carbon: Glucose, Fructose, Galactose Saturated: all it can fill, all single bonds, solid at room temperature and less healthy Unsaturated: room for more Hydrogens, Double bonds, plants, liquid at room temp, healthier Steriods: four fused rings GLUCOSE + FRUCTOSE  DEHYDRATION SYNTHESIS  SUCROSE Protein Structure: Primary: chain of amino acids held by peptide bonds, Secondary: formed into Helix or Pleated Sheet, Tertiary: turns into a globular protein (has all bonds) and makes a special disulfide bridge, Quaternary: functional, groups of subunits motifs: repetitive pattern domain: functional units within a larger structure Phospholipids: form the core of all membranes; Glycerol: 3 carbon alcohol, Fatty Acids: long chains of –CH2 groups, Phosphate Group: attached to one end of the glycerol Prokaryote Cells: do not have membrane bound cells, and no nucleus. Consists of Bacteria and Archaea (binary fission)(lack peptidoglycan) some prokaryotes have flagella, which is also able to rotate like a wheel for locomotion PLANTS DON’T HAVE: flagella, centrioles ANIMALS DON’T HAVE: cell wall, chloroplasts, a central vacuole (have small vesicles) Eukaryotic Organelles and Functions Double membrane organelles: Nucleus, Mitochondria and chloroplasts Mitochondria + Chloroplasts=have own DNA Ribosomes: carry out protein synthesis Nucleus: has chromosomes—compact units that consist of DNA wound around proteins Nucleolus: where intensive synthesis of rRNA takes place Smooth ER: makes lipids, and detoxifies alcohol and drugs Rough ER: has ribosomes on it, the proteins on here are planned to be exported and sent to lysosomes Golgi Apparatus: manufacturing process, consists of membranous sacs called cisternae Proteins synthesized by RER ribosome, transported within vesicles that bud off the rough ER, then travel to cis face—modified and packaged into vesicles that bud off the trans face. Vesicles leave the trans face transport proteins to other locations releasing their contents to the extra cellular environment Lysosomes: “suicide sacs” and helps digest by phagocytosis; come from Golgi, recycle old organelles Mitochondria: double-membrane, inner folded into cristae for surface area, the matrix is in the inside of cristae and an intermembrane space which is between the cristae and outermembrane membrane; have own DNA! Chloroplasts: manufacture their own food, gives plants the green color. Include Thylakoids- membranous organs in flattened sac, Stroma—the fluid outside, Granum: stacks of thylakoids Plastids: amlyoplast(starch storage), chloroplasts (chlorophyll), Chromoplast (non-green pigments) Vacuoles: ONLY IN PLANTS, tonoplast membrane; it contains channels for water to help maintain osmotic balance Endosymbiosis: proposing that eukaryotic organelles today came from Cytoskeleton: 9+2 arrangement, network of fibers through the cytoplasm Microtubules: largest, shape the cell and help with movement; Intermediate filaments: most durable, composed of overlapping staggered tetramers of protein, which are bundled into cables Actin filaments: composed of two protein chains intertwined, each subunit on the chain is the protein actin Centrioles: barrel-shaped organelles found in cells of animals; surrounding area is the centrosome Kinesin: uses ATP to power its movement toward the cell periphery Myosin: muscle contraction Dynein: directs movement in the opposite direction along microtubules Primary wall—Middle lamella---secondary wall; consists of plasmodesmata bars going across membranes Animals have the extracellular matrix made up of glycoproteins acting like a cell wall Microbodies: enzyme-bearing, membrane-enclosed vesicles Peroxisome: contains enzymes that catalyze the removal of electrons and associated H atoms Glyoxysome: plant cells; contains enzymes that convert fats into carbs CELL MEMBRANE AND DIFFUSION Phospholipids: foundation for cell’s membrane; not very soluble in water Fluid Mosaic Model: a mosaic of proteins floats in or on the fluid lipid bilayer --Cholesterol is in the bilayer Transmembrane proteins (collection of proteins that allow substances to pass through) Proteins embedded into the membrane—Integral membrane proteins Peripheral membrane proteins—associated with the membrane but not part of its structure The ER adds sugar molecules to proteins and lipids changing them to glycoproteins and glycolipids Backbone is from the 3 carbon polyalcohol glycerol HEADS= HYDROPHILIC TAILS=HYDROPHOBIC Transporters: allowing only certain substances in and out/Enzymes: attached to the membrane where chemical reactions are carried out/Cell Surface receptors: detecting chemicals/Identity markers: identify themselves, “ID tags” Cell-to-Cell adhesions proteins: use proteins to glue themselves to one another Attachments to the cytoskeleton: proteins that interact with other cells and anchored to the cytoskeleton Passive Transport: moving in and out without energy! Diffusion: movement from high  low Channel proteins: only passive, hydrophilic interior that provides an aqueous channel through which polar molecules can pass Carrier proteins: (active & passive) bind to the molecule they assist--makes the membrane: selectively permeable Ion channels: a hydrated interior gated channels: opened or closed in response to stimuli Facilitated diffusion: movement across membrane with carrier protein, does not use energy, but speeds up movement Active transport: low  high concentration NEEDS ENERGY, USES ATP Water is the solvent and the substances dissolved in water are the solutes Osmosis: net diffusion of water across a membrane toward a higher solute concentration Hypertonic: solution with higher concentration hypotonic: solution with lower concentration Chromosomes consist of chromatin; DNA duplex wound around proteins called histones, these are called nucleosomes. Finalized into loops; cohesions hold together two DNA molecules (chromosomes). Kinetochores—package of proteins (attachment); 2 chromatids make a chromosome, but when the cohesin is dissolved (which splits the chromosome) then each one is called a chromosome Cell Cycle = G1 (growth phase; filling the gap between cytokinesis and DNA synthesis)(9hr)  S (synthesis; cell synthesizes a replica of the genome)(10hr)  G2 (preparations for separation of the newly replicated genome)(2 hr)  M (mitosis; spindle apparatus assembles, binds to the chromosomes and moves the chromatids apart) (1 hr)  C (cytokinesis; cytoplasm divides, creating 2 daughter cells) Interphase G2 before mitosis Mitosis (somatic cells): Prophase (chromosomes condense, spindle forms)  Prometaphase (chromosomes attach to microtubules)  Metaphase (chromosomes align)  Anaphase (chromosomes pulled to poles)  Telophase (nuclear envelopes reform)  Cytokinesis (cleavage, splits) Spindle proteins: push poles apart before cytokinesis **Cancer is a failure of cell cycle control ** Produced cells are close to the same as mother cell Meiosis (sex cells): Prophase I (chromosomes condense  Metaphase I (pairs align)  Anaphase I (pairs pulled apart)  Telophase I (separating to each pole and closing off—2 cells)  Prophase II (a new spindle forms)  Metaphase II (line up)  Anaphase II (pulled to poles)  Telophase II (membranes re-form) *No 2 cells are alike Results in 4 haploid daughter cells (not identical) Sexual Reproduction—Meiosis (producing 4 haploid cells—each with half the number of chromosomes) The cells produced are quantitatively and qualitatively different from mother cell. no DNA replication; Independent assortment(in 1 st metaphase) : increases genetic variability; due to randomness in metaphase ; Random fertilization can also give genetic variation Heredity Monohybrid—x/4 dihybrid—x/16 Trihybrid—x/64 Tetrahybrid—x/256 Gene Action: Polygenic inheritance—more than one gene affects a trait (nose length) Epistasis— one gene controls another Alleles—alternative form of a gene gene—information for traits passed down from parents Pleioptrophy—one gene, but multiple effects (sickle cell anemia) Codominance—both genes expressed (blood group) Sex Determination  humans (xx, xy); Birds (zw, zz); grasshoppers (xx, xo); honeybees (diploid, haploid) Crossing over—exchanges alleles; occurs between two loci, leads to production of recombinant chromosomes (Prophase) Huntington’s Disease and Hypercholesterolemia are the only dominant genetic disorder Hemophilia and Muscular dystrophy are x-linked recessive Genetic Material Transformation—transfer of viruses from cell to another Two-rings (larger): adenine & guanine(has carboxyl group) One ring: thymine, cytosine & uracil (replaces T in RNA) Phosphodiester bond—links sugars together  DNA helix—twisting due to hydrogen bonds Double helix—rotating with each other, but in opposite directions; major groove(where receptors fit in) Helicase—unwinds the helix Primase—synthesizes RNA primers DNA gyrase —relieves torque Single-strand binding protein—stabilizes single-stranded regions DNA poly I—erases primer and fills gaps DNA poly III—synthesizes DNA and adds to the 3’ end (can’t go in from 5’ end) DNA ligase—joins the ends of DNA segments; DNA repair REPLICATION  DNA gyrase creates 2 template strands  from 5’ to 3’—lagging strand—by discontinuous synthesis—begins with primase—synthesizes RNA primer—deleted by DNA poly I—fills gaps between Okazaki fragments—fragments linked by ligase/nucleotides linked by DNA poly III— strands rewind forming sister chromatids--  3’ to 5’ leading strand—by continuous synthesis— nucleotides linked by DNA poly III—errors corrected by nucleases Promoters—provide attachment sites for enzymes. RNA poly—makes RNA transcript Terminators—DNA sequences At the end—there aren’t any more primers (it gets shorter and shorter) so telomerase comes to fill the gaps Genes DNA  RNA = transcription RNA  Protein=translation Transcription=produces an RNA copy of the information in DNA; template stand—stand that is copied; coding stand—strand not used as a template; EX: coding 5’ TCAGCCGTCAGCT 3’ --DNA Template 3’ AGTCGGCAGTCGA 5’ –DNA Coding 5’ UCAGCCGUCAGCU 3’ -- mRNA **tRNA: interacts with amino acids and RNA Initiation complex—formed containing mRNA and initiator tRNA bound to the amino acid methionine (start) Eukaryotes—5’ cap, where methylated GTP is added. snRNPs—composed of snRNA and protein Then snRNPs cluster together with other proteins to form splicesomes—which take out introns poly-A tail—a long chain of adenine residues to the 3’ end of the transcript End product—mature mRNA—protein tRNA charging reaction—amino acids activated; aa reacts with ATP; aa—AMP remains bound to the enzyme; tRNA binds to the enzyme; transfers aa from AMP to the tRNA producing a charged tRNA and AMP A site—entrance of the new tRNA with amino acid P site—binds to the tRNA attached o the growing peptide chain A site—carrying the next amino acid to be added E site—binds the tRNA that carried the previous amino acid added. tRNA uses GTP (kreb’s cycle) GENE EXPRESSION Binding motifs Regulatory proteins—modulating the ability of RNA polymerase to bind to the promoter Helix-turn-helix—binds to DNA using one a helix to interact with the major groove; allows regulatory proteins to slip into two protions of the major groove in DNA—strong attachment Homeodomain—common in proteins that regulate development and similar amino acid sequences Zine finger—two a helices that interact with the major groove; act like fingers of a hand holding DNA Leucine zipper—hold two subunits in a multisubunit protein together (fit into Y region) Operator—on/off switch lac operon—won’t work without repressor CAP—speeds up process Tryptophan builds up and binds to repressor to change the shape of the protein and attaches to active site to shuts it off Glucose low=not much glycolysis happening=no ATP formed so the materials turns into cAMP Inducer exclusion—high glucose levels prevent lactose from entering the cell and keeps repressor bound to DNA Initiation—TAFs recruit RNA poly II; proteins attach to TATA boxes—then bring cofactors to it—initiate/ make mRNA Enhancers—an activator binds to it which allows it to interact with the trancription factors with RNA poly—initiates Methylation & histone—prevents code from being read Control with: enhancer/activators/repressors RNA interferences—Dicer enzyme makes small RNA—miRNA(bonds to mRNA/base pairing) & siRNA(works with RISC enzyme and degrades mRNA pieces that are complementary) Ubiquitin— trigger for destruction CONTROLS OF GENE EXPRESSION : Initiation—RNA splicing—passage through nuclear membrane— destruction of transcript—protein synthesis—post-mod. Alternative Splicing—control activity/ introns spliced out/ genes read in different ways to produce many different combos. Recombinant DNA—a single DNA molecule made from 2 different sources Restriction endonucleases—the enzymes that were able to cleave DNA at specific sites; produce DNA fragments DNA polymerase—brings the DNA together **DNA IS A NEGATIVE CHARGE DNA ligase—joins DNA fragments (like sticky ends) reforming the phosphodiester bonds Gel electrophoresis—separating DNA fragments  the gel/electrical field allows the smaller one to move faster and farther because of the pos. and neg. ends ** Sticky ends help produce recombinant molecules Transformation-placing foreign DNA into a different cell; transgenic-transformed cell to produce part/all of an organism Plasmids—small; circular DNA; usually for cloning small pieces; *need an origin of replication *a selectable marker Phage—larger; linear DNA; viruses that infect bacterial cells; usually kills the cell **human insulin, tobacco DNA library—collection of DNAs in a vector that taken together represent the complex mixture of DNA Genomic library—entire genome in a vector Reverse transcriptase—enzymes that convert mRNA into double-stranded DNA resulting in a cDNA; to make a library of only expressed sequences representing smaller amount of DNA. cDNA—DNA copies of mRNAs; can be cloned into bacterial cells; complementary base pairing; used for libraries and useful in representing the genes expressed in different cells RFLPs—easier way to see variation in fragments of DNA; *different DNA sequences with different mutations *DNA is cut *put into gel electrophoresis to analysis *DNA sequencing —more info about genes and genomes Polymerase Chain Reaction (PCR)—a sample is heated to denature DNA  then cooled to allow annealing  heated again to extend primers (DNA synthesis) (like double: 12 and 24)—allows investigation of small DNA samples **usually takes 30-40 times to produce the amplified DNA fragment Genetic Engineering—cloning individual genes for analysis; transgenic animal—an animal containing a gene that has been introduced without the use of conventional breeding; in vitro—creating mutations at any site in a cloned gene Southern Blot—used to verify the presence or absence of a specific nucleotide sequence in the DNA from different sources -DNA is isolated; then fragments loaded onto gel and separated by electrophoresis; smaller fragments migrating faster; then made visible with ethidium bromide; DNA transferred from fragile gel to nylon filter **Golden Rice—genes were added to rice genome to all expression of carotene pathway. **bacteria produce human insulin. Interspecific—genes transferred by viruses between species; leads to transformation Intraspecific—within species; jumping—transposons; between sister chromatids—meiosis I; result of sex—fertilization; even change numbers—polyploidy Genomics Genetic maps—maps that place the location of genes on chromosomes based on recombination frequency Physical maps—use landmarks within DNAs sequences *Restriction enzymes—used to create a physical map Alternative splicing—creating many genes are read in different ways leading to generate different ways to live Cellular Mechanisms Development—process of systematic gene-directed changes (life cycle) Cell Division—(zygote/cell  individual)—no G1 and G2 phases in early cell stages—Cell cycle: G1, S, G2, M, and C Totipotent—can become any cell type and develop into a whole organism Pluripotent—can become cells of any germ layer, but cannot develop into a whole organism Ectoderm (skin); Mesoderm (muscle); Endoderm (internal tissue) Multipotent—can give rise to only a few cell lines Stem Cells—pluripotent: embryonic stem cells; multipotent: adult stem cells Determination—differentiation due to proteins that are synthesized Cytoplasmic determinates—asymmetrical inheritance of cytoplasmic inclusions *bilateral larvae Induction—one cell type inducing neighboring cells to develop another way; interacting w/ DNA to turn on/off genes Cell Fate—inherits or mutates something in the beginning to effect growth and production M or e sp ec if ic