Transformation Protocol

Study Guide

Concept 2.2- An element’s properties depend on the strength of its atoms

• Subatomic Particles
  • Atom smallest unit of element
  • Nucleus made of + protons and uncharged neutrons, with cloud of – electrons outside
• Atomic Number and Mass
  • In neutral atom, # of electrons= # of protons
• Isotopes
  • Most elements have 2+ isotopes
  • Some are unstable and give off particles and energy as radioactivity
• Energy Levels of Electrons
  • Electrons occupy specific energy levels, each of which can be represent by and electron shells
• Electron Configuration and Chemical Properties
  • Electron configuration determines the chemical behavior of an atom
  • Chemical behavior depends on the number of valence electrons
  • Atom with an incomplete valence shell is reactive
• Electron Orbitals
  • Electrons move within orbitals
  • Orbitals are 3-D spaces with specific shapes located within each successive shell

Concept 2.3- The formation and function of molecules depend on chemical bonding between atoms

• Covalent Bonds
  • The sharing of a pair of valence electrons by two atoms
  • Molecules consist of two or more covalently bonded atoms
  • Electrons of a polar covalent bonds are pulled closer to the more electronegative atom
  • A covalent bond is nonpolar if both atoms are the same so they are equally electronegative
• Ionic Bonds
  • Two atoms may differ so much in electronegatvity that one or more electrons are actually transfered from one atom to the other
    • NaCl
  • Result in – ion (anion) and + ion (cation)
• < div style=”MARGIN-BOTTOM: 0in”>Weak Chemical Bonds
  • Hydrogen bond
    • Bond between one electronegative atom and a hydrogen atom that is covalently linked to an atom that is electronegative
  • Van der Waals interactions
    • Occur when transiently positive and negative regions of molecules attract each other
• Molecular Shape and Function
  • Molecules shape is determined by the position of its atoms’ valence orbitals

Concept 3.1- The polarity of water molecules results in hydrogen bonding

• Hydrogen Bonding in Water
  • Forms when the oxygen of one water molecule is electrically attracted to the hydrogent of a nearby molecule

Concept 3.2- Four emergent properties of water contribute to Earth’s fitness for life

• Cohesion
  • Hydrogen bonding keeps water molecules close to each other
  • Helps pull water upward in the microsco pic vessels of plants
  • Hydrogen bonding also responsible for water tension
• Moderation of Temperature
  • H-bonding gives water a high specific heat
  • Heat is absorbed when h-bonds break and is released when h-bonds form
    • Minimizes temperature fluctuations
  • Evaporative cooling is based on water’s high heat of vaporization
• Insulation of Bodies of Water by Floating Ice
  • Ice is less dense than liquid water due to it being more organized
  • Allows organisms to live in icy climates under ice
• The Solvent of Life
  • Hydophillic substances have an affinity for water, while hydrophobic do not

Concept 4.3- Functional groups are the parts of molecules involved in chemical reactions

• Functional Groups Most Important in the Chemistry of Life
  • Hydroxyl (-OH)
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  • Polar, helps compounds dissolve in water
• Carbonyl (>CO)
  • Can be at end of of a carbon skeleton (aldehyde) or within it (ketone)
• Carboxyl (-COOH)
  • Usually founds in carboxyllic acids
• Amino (-NH2)
  • Can accept a proton so it works as a base
• Sulfhydryl (-SH)
  • Helps stabilize the structure of some proteins
• Phosphate(-OPO32-)
  • Important role in the transfer of energy

ATP: An Important Source of Energy for Cellular Processes

• When a phosphate group splits off from ATP, energy is released that can be used by cell

The Chemical Element of Life: A Review

• Living Matter is made of carbon, oxygen, hydrogen, nitrogen, and some sulfur and phosphorus mostly

Concept 5.2- Carbohydrates serve as fuel and building material

• Sugars
  • Smallest carbohydrate, serve as fuel and carbon sources
  • Used for fuel, converted to other organic molecules, or combined into polymers
  • Disachharides consist of 2 monosaccharides connected by a glycosidic linkage
• Polysaccharides
  • Polymers of sugars, have storage and structural roles
    • Starch is used in plants and animals to store glucose
    • Used in plants for cellulose which make cell walls

Concept 5.4- Proteins have many structures, resulting in a wide range of functions

• Polypeptides
  • Polymer of amino acids connected in a specific sequence
  • Proteins consist of 1 or more polypeptide chains folded into a specific 3-D conformation
  • The carboxyl and amino groups of adjacent amino acids link together in peptide bonds
• Protein Conformation and Function
  • Primary structure: unique sequence of amino acids
  • Secondary structure: Folding or coiling of the polypeptide into repeating configurations
  • Tertiary structure: the overall 3-D shape of a polypeptide

Concept 5.3- Lipids are a diverse group of hydrophobic molecules

• Fats
  • Store large amounts of energy
  • Also known as triacylglycerols- a glycerol molecule joined to 3 fatty acids by dehydration reactions
  • Saturated fatty acids have the maximum number of hydrogen atoms
  • Unsaturated fatty acids have one or more double bonds in their hydrocarbon chains
• Phospholipids
  • Major components of cell membranes
  • Consist of 2 fatty acids and a phosphate group linked to glycerol
    • Rudolph
• Steroids
  • Include holesterol and certai n hormones
  • Basic structre of four fused rings of carbon atoms

Concept 6.4- The endomembrane system regulates protein traffic and performs metabolic functions in the cell

• Membranes
  • Membranes of the endomembrane system are connect by physical coninuity or through transport vesicles
• The Endoplasmic Reticulum: Biosynthetic Factory
  • Smooth ER synthesizes lipids, metabolizes carbohydrates, stores calcium, and detoxifies poisons
  • Rough ER has bound ribosomes and produces proteins and membranes, and are then distributed by transport vesicles
• The Golgi Apparatus: Shipping and Receiving Center
  • Proteins are transported from the ER and are then modified, sorted, and released in transport vesicles
• Lysosomes: Digestive Compartments
  • Sacs of hydrolytic enzymes that break down ingested substances and cell macromolecules for recylcing
• Vacuoles: Diverse Maintenance Compartments
  • For plants, functions in digestion, storage, waste disposal, cell growth, and protection

Concept 6.5- Mitochondria and chloroplasts change energy from one form to another

• Mitochondria: Chemical Energy Conversion
  • Site of cellular respiration, have an outer membrane and an inner membrane that is folded into cristae
• Chloroplasts: Capture of Light Energy
  • Contain pigments that function in phosynthesis
  • 2+ membranes surround fluid stroma, which contains thylakoids stacked into grana
• Peroxisomes: Oxidation
  • Produce hydrogen peroxide and convert it to water

Concept 6.6- The cytoskeleton is a network of fibers that organizes structures and activities in the cell

• Roles of the Cytoskeleton: Support, Motility, and Regulation
  • Functions in structural support for the cell, motility, and signal transmission
• Components of the Cytoskeleton
  • Microtubules shape the cell, guide movement of organelles, and help separate the chromosome copies in dividing cells
  • Cilia and flagella are motile appendages containing microtubules
  • Microfilaments are thin rods built from actin
    • Function in muscle contraction, amoeboid movement, cytoplasmic streaming, and support for microvilli

Concept 7.1- Cellular membranes are fluid mosaics of lipids and proteins

• Membrane Models: Scientific Inquiry
  • Davson-Danielli sandwich model of the membrane has been replaced by the fluid mosaic model
  • Amphipathic proteins are embedded in the phospholipid bilayer
• The Fluidity of Membranes
  • Phopholipids and proteins move laterally within the membrane
  • Cholesterol and unsaturated hydrocabon tales in the phospholipids affect fluidity
• Membrane Proteins and Their Functions
  • Integral proteins are embedded in the lipid bilayer
  • Peripheral proteins are attached to the surfaces
  • Functions in transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining and attachment to the cytoskeleton and extracellular matrix
• The Role of Membrane Carbohydrates in Cell-Cell Recognition
  • Short chains of sugars are linked to proteins and lipids on the exterior side of the plasma membrane
    • Ineract with the surface molecules of other cells
• Synthesis and Sidedness of Membranes
  • Membrane proteins and lipids are synthesized in the ER and modified in the ER and Golgi apparatus

Concept 7.3- Passive transport is diffusion of a substance across a membrane with no energy investment

• Diffusion
  • The spontaneous movement of a substance down its concentration gradient
• Effects of Osmosis on Water Balance
  • Water flows across a membrane from the side where solute is less concentrated (hypotonic) to where it is more concen trated (hypertonic)
  • Isotonic when concentrations are equal and no net osmosis occurs
  • Cell walls are elastic so the cell doesn’t burst when in a hypotonic environment
• Facilitated Diffusion: Passive Transport Aided by Proteins
  • Transport protein speeds the movement of water or a solute across a membrane down its concentration gradient

Concept 7.4- Active transport uses energy to move solutes against their gradients

• The Need for Energy in Active Transport
  • Specific membrane proteins use energy, usually ATP, to do the work of active transport
• Maintenance of Membrane Potential by Ion Pumps
  • Ions can have both a concentraion and electrical gradient
  • Forces combine in the electrochemical graient, which determines the net direction of ionic diffusion
    • Example: NaK pumps
• Cotransport; Coupled Transport by a Membrane Protein
  • One solute’s Cdownhill” diffusion drives the other’s “uphill” transport

Concept 8.5- Regulation of enzyme activity helps control metabolism

• Allosteric Regulation of Enzymes
  • They change shape when regulatory molecules, activators or inhibitors, bind to specific regulatory sites, affecting enzymatic functional
• Specific Localization of Enzymes Within the Cell
  • Some enzymes are grouped into complexes, some are incorporated into membranes while others are contained inside organelles

Concept 9.1- Catabolic pathways yield energy by oxidizing organic fuels

• Catabolic Pathways and Production of ATP
  • The breakdown of glucose and other organic fuels is exergonic
  • Glucose + O2 –> H20 + CO2 + ATP + Heat
• Redox Reactions: Oxidation and Reduction
  • Cell taps energy stored in food molecules through redox reactions
    • One substance partially or totally shifts electrons to another; substance receiving electrons is reduced while substance losing electrons is oxidized
  • During cellular respiration, glucose is oxidized to CO2, and 02 is reduced to H20
  • Electrons from organic compounds are usually passed first to NAD+, reducing it to NADH
    • NADH passes the electrons to an electron transport chain which conducts them to 02 in energy releasing steps
    • Energy released is used to make ATP
• The Stages of Cellular Respiration
  • Glycolysis and the citric acid cycle supply electrons to the electron transport chain
    • Drives oxidative phosphorylation which generates ATP

Concept 9.3- The citric acid cycle completes the energy-yielding oxidation of organic molecules

• Cytric Acid Cycle
  • Pyruvate is imported into the mitochondrion and its conversion to acetyl CoA joins the 4-carbon oxaloacetate, forming the 6-carbon citrate, which is degraded back to oxaloacetate
  • Cycle releases 2 CO2, forms 1 ATP, and passes electrons to NAD+ and FAD,=2 0yielding 3 NADH and 1 FADH2 per turn

Concept 9.4- During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis

• Electron Donation
  • NADH and FADH2 donate electrons to the electron transport chain, which powers ATP synthesis via oxidative phosphorylation
• The Pathway of Electron Transport
  • In the electron trasnport chain, electrons from NADH and FADH2 lose energy and result in making water molecules
• Chemiosmosis: The Energy-Coupling Mechanism
  • At certain steps along the electron transport chain, electron transfer causes protein complex to move H+ from the mitochondrial matrix to the intermembrane space
    • Stores energy as a proton-movie force
  • As H+ diffuses back into the matrix through ATP synthase, its passage drives the phosphorylation of ADP
• An Accounting of ATP Production by Cellular Respiration
  • About 40% of the energy stored in a glucose molecule is transfreed to ATP during cellular respiration, produc tin a maximum of about 38 ATP

Concept 10.2- The light reactions convert solar energy to the chemical energy of ATP and NADPH

• The Nature of Sunlight
  • Light is a form of electromagnetic energy
• Photosynthetic Pigments: The Light Receptors
  • A pigment absorbs visible light of specific wavelengths
  • Chlorophyll a is the main photosynthetic pigment in plants which receives energy from accessory pigments
• Excitation of Chlorophyll by Light
  • A pigment goes from a ground state to an excited state when a photon boosts one of its electrons to a higher-energy orbital
    • Unstable
  • Electrons from isolated pigments tend to fall back to the ground state, giving off heat
• A Photosystem: A Reaction Center Associated with Light-Harvesting Complexes
  • A photosystem is composed of a reaction center surrounded by light-harvesting complexes that funnel the energy of photons to the reaction center
  • 0D
  • When a reaction-center chlorophyll a molecule absorbs energy, one of its electrons gets bumped up to the primary electron acceptor
  • Photosystem I contains P700 chlorophyll a molecules while photosystem II contains P680
• Noncyclic Electron Flow
  • Noncyclic electron flow produces NADPH, ATP, and oxygen
• Cyclic Electron Flow
  • Cyclic electron flow employs only photosystem I, producing ATP but no NADH or oxygen
• A Comparison of Chemiosmosis in Chloroplasts and Mitochondria
  • In both organelles, the redox reactions of electron transport chains generate an H+ gradient acrross a membrane
  • ATP synthase uses the proton-motive force to make ATP

Concept 10.3- The Calvin Cycle uses ATP and NADPH to convert CO2 to sugar

• The Calvin Cycle
  • Occurs in the stroma and consists of carbon fixation, reduction, and regeneration of the CO2 acceptor
  • Using electrons from NADPH and20energy from ATP, the cycle synthesizes a 3-carbon sugar
  • Most of the G3P is reused in the cycle, but some exits the cycle and is converted to glucose

Concept 11.2- Reception: A signal molecule binds to a receptor protein, causing it to change shape

• Reception
  • The binding between signal molecule (ligand) and receptor is highly specific
  • A conformation change in a receptor is often the initial transduction of the signal
• Intracellular Receptors
  • Cytoplasmic or nuclear proteins
  • Signal molecules that are small or hydrophobic that can cross the plasma membrane use these receptors
• Receptors in the Plasma Membrane
  • G-protein-linked receptor is a membrane receptor that works with the help of a cytoplasmic G protein
  • Ligand binding activates the receptor, which then activates a specific G protein, which activates another protein
    • Creases a signal transduction pathway
  • Receptor tyrosine kinases react to the binding of signal molecules by forming dimers
    • Adding phosphate groups to tyrosines on the cytoplasmic side of the other subunit of the dimer
  • Relay proteins in the cell can then be activated by binding to different phospohorylated tyrosines, allowing this receptor to trigger several pathways at once
  • Specific signal molecules cause ligand-gated ion channels in a membrane to open or close, regulating the flow of specific ions

Concept 12.1- Cell division results in genetically identical daughter cells

• Cell Division
  • Cells duplicate their genetic material before they divide, ensuring that each daughter cell receives an exact copy of the genetic material, DNA
• Cellular Organization of the Genetic Material
  • DNA is partitioned among chromosomes
  • Eukaryotic chromosomes consist of chromatin, a complex of DNA and protein that condenses during mitosis
  • In animals, gametes have one set of chromosomes and somatic cells have two sets
• =0 A
• Distribution of Chromosomes During Cell Division
  • For cell division, chromosomes replicate, each 1 consisting of 2 identical sister chromatids
  • The chromatids separate during cell division, becoming the chromosomes of the new daughter cells
  • Eukaryotic cell division consists of mitosis and cytokinesis

Concept 12.2- The mitotic phase alternates with interphase in the cell cycle

• Phases of the Cell Cycle
  • Between divisions, cells are in interphase, the G1, S, and G2 phases
    • Cell grows throught interphase, but DNA is replicated only during the synthesis phase
  • Mitosis and cytokinesis make up the mitotic (M) phase of the cell cycle
  • Mitosis is a continuous process, often described as occuring in 5 stages
    • Prophase, Prometaphase, Metaphase, Anaphase, and Telophase
• The Mitotic Spindle: A Closer Look
  • The mitotic spindle is an a pparatus of microtubules that controls chromosome movement during mitosis
  • The spindle arises from the centrosomes and includes spindle microtubules and asters
  • In anaphase, sister chromatids separate and move along the kinetochore microtubules toward opposite end of the cell
  • Meanwhile, nonkinetochore microtubules from opposite poles overlap and push against each other, elongating the cell
  • In telophase, genetically identical daughter nuclei form at opposite ends of the cell
• Cytokinesis: A Closer Look
  • Mitosis is usually followed by cytokinesis
  • Animal cells carry out cytokinesis by cleaving, and plant cells form a cell plate
• Binary Fission
  • The bacterial chromosome replicates and the 2 daughter chromosomes actively move apart
• The Evolution of Mitosis
  • Since prokaryotes preceded eukaryotes by more than a billion years, it is likely that mitosis evolved from prokaryotic cell division
  • Certain protists exhibit types of cell division that see intermediat e between binary fission and the process of mitosis carried out by most eukaryotic cells

Concept 13.3- Meiosis reduces the number of chromosome sets from diploid to haploid

• The Stages of Meiosis
  • Two cell divisions of meiosis produce 4 haplod daughter cells
  • The number of chromosome sets is reduced from diploid to haploid during meiosis I
• A Comparison of Mitosis and Meiosis
  • Meiosis is distinguished from mitosis by three events of meiosis I
    • Synapsis, which is associated with crossing over; positioning of paired homologous chromosomes (tetrads) on the metaphase plate; and movement of the 2 chromosomes of each homologous pair to opposite poles during anaphase I
  • Meiosis II separates the sister chromatids

Concept 14.1- Mendel used the scientific approach to identify two laws of inheritance

• Mendel’s Experiment, Quantitative Approach

Gregor Mendel formulated a particulate theory of inheritance based on experiments with garden peas, carried out in the 1860s

• Showed that parents pass on to their offspring discrete genes that retain their identity through the generations
• The Law of Segregation
  • States that the two alleles of a gene separate during gamete formation so that a sperm or an egg carriers only one allele of each pair
  • Proposed this law to explain the 3:1 ratio of F2 phenotypes he observed when monohybrids self-pollinated
  • Get one allele from each parent
  • Dominant gene masks over recessive gene if heterozygous for trait
• The Law of Independent Assortment
  • States that each pair of alleles segregates into gametes independently of other pairs
  • Used to explain dihybrid cross (9:3:3:1)

Concept 14.3- Inheritance patterns are often more complex than predicted by simple Mendelian genetics

• Extending Mendelian Genetic for a Single Gene
  • For a gene with complete dominance of one allele, the hertozygoues phenotype is the same as that for the homozygous dominant pheontype
  • For a gene with codominance of both alleles, both phenotypes are expressed in heterozygotes
  • For a gene with incomplete dominance of either allele, the heterozygous phenotpe is intermediate between the 2 homozygous phenotypes
  • Many genes exist in multiple alles in a population
  • Pleiotropy is the ability of a single gene to affect multiple phenotypic characters
• Extending Mendelian Genetics for Two or More Genes
  • In epistatis, one gene affects the expression of another gene
  • In polygenic inheritance, a single phenotypic character is affected by two or more genes
  • Characters influenced by multiple geners are often quantitative, meaning they vary continuously
• Nature and Nurture: The Environmental Impact on Phenotype
  • Expression of a genotype can be affected by environmental influences
  • The phenotypic range of a particular genotype is called its norm of reaction
  • Polygenic characters that are also influenced by the environment are called multifactorial characters
• Integrating a Mendelian View of Heredity and Variation
  • An organism’s overall phenotype, including its physical appearance, internal anatomy, physiology, and behavior, reflects its overall genotope and uniqure environmental history
  • Even in more complex inheritance patterns, Mendel’s 2 laws still apply

Concept 14.4- Many human traits follow Mendelian patterns of inheritance

• Pedigree Analysis
  • Family pedigrees can be used to deduce the possible genotpes of individuals and make predictions about future offspring
• Recessively Inherited Disorders
  • Tay-Sachs disease, cystic fibrosis, sickle-cell disease
• Dominantly Inherited Disorders
  • Lethal dominant alleles are eliminated from the population if affected people di e before reproducing
  • Huntington’s disease
• Multifactorial Disorders
  • Most forms of cancer and heart disease, have both genetic and environmental components

Concept 15.2- Linked genes tend to be inherited together because they are located near each other on the same chromosome

• How Linkage Affects Inheritance: Scientific Inquiry
  • Each chromosome has hundreds or thousands of genes
  • Genes on the same chromosome whose alleles are so together that they do not assort independently are said to be linked
  • The alleles of unlinked genes are either on separate chromosomes or so far apart on the same chromosome that they assort independently
• Genetic Recombination and Linkage
  • Recombinant offspring exhibit new combinations of traits inherited from two parents
  • Due to the independent assortment of chromosomes and random fertilization, unlinked genes e xhibit a 50% frequency of recombination
  • Even with crossing over between nonsister chromatids during the first meiotic division, linked genes exhibit recombination frequencies less than 50%
• Linkage Mapping Using Recombination Data
  • Geneticists can deduce the order of genes on a chromosome and the relative distances between them from recombination frequencies observed in genetic crosses
  • In general, the farther apart genes are on a chromosome, the more likely they are to be separated during crossing over

Concept 15.5- Some inheritance patterns are exceptions to the standard chromosome theory

• Genomic Imprinting
  • In mammals, the phenotypic effects of certain genes depend on which allele is inherited from the mother and which is inherited from the father
  • Imprints are formed during gamete production, with the result that one allele (either maternal or paternal) is not expressed in offspring
  • Most imprinted genes now known play a role in embryonic development
• Inheritance of Organelle Genes
  • The inheritance of traits controlled by the genes present in mitochondria and chloroplasts depends solely on the maternal parent because the zygote’s cytoplasm comes from the egg
  • Some diseases affect the nervous and muscular systems are caused by defects in mitchondrial genes that prevent cells from making enough ATP

Concept 16.1- DNA is the genetic material

• The Search for the Genetic Material: Scientific Inquiry

Experiments with bacteria and with phages provided the first strong evidence the genetic material is DNA

• Building a Structural Model of DNA: Scientific Inquiry

Watson and Crick deduced that DNA is a double helix

Two antiparallel sugar-phosphate chains wind around the outside of the molecule; the nitrogenous bases project into the interior, where they h-bond in specific pairs

A with T; G with C

Concept 16.2- Many proteins work together in DNA replication and repair

• The Basic Principle: Base Pairing to a Template Strand

DNA replication is semiconservative: The parent molecule unwinds, and each strand then serves as a template for the synthesis of a new strand according to base-pairing rules

• DNA Replication: A Closer Look

DNA replication begins at origins of replication

Y-shaped replication forks form at opposite ends of a replication bubble, where the 2 DNA strands separate

DNA synthesis starts at the 3′ end of an RNA primer, a short polynucleotide complementary to the template strand

DNA polymerases catalyze the synthesis of new DNA strands, working in the 5′–>3′ direction

The leading strand is synthesized continuously, and the lagging strand is synthesized in short segments, called Okazaki fragments

Fragments are joined together by DNA ligase

• Proofreading and Repairing DNA

DNA polymerases proofreads newly made DNA, replacing any incorrect nucleotides

In mismatch repair of DNA, repair enzymes correct errors in base pairing

In nucleotide excision repair, enzymes cut out and replace damaged stretches of DNA

• Replicating the End of DNA Molecules

The ends of eukaryotic chromosomal DNA get shorter with each round of replication

The presence of telomeres, repetitive sequences at the ends of linear DNA molecules, postpones the erosion of genes

Telomerase catalyzes the lengthening of telomeres in germ cells

Concept 17.3- Eukaryotic cells modify RNA after transcription

• Alteration of mRNA Ends
  • Eukaryotic mRNA molecules are processed before leaving the nucleus by modification of their ends and by RNA splicing
  • The 5′ end receives a modified nucleotide cap, and then 3′ end a poly-A tail
• Split Genes and RNA Splicing
  • Most eukaryotic genes have introns interspersed among the coding regions, the exons
  • In RNA splicing, introns are removed and exons joined
  • RNA splicing is ca rried out by spliceosomes, but in some cases, RNA catalyzes splicing
  • Catalytic RNA molecules are ribozymes

Concept 17.7- Point mutations can affect protein structure and function

• Types of Point Mutations
  • A point mutation is a change in one DNA base pair, which may lead to production of a nonfunctioning protein or no protein at all
  • Base-pair substitutions can cause missense or nonsense mutations
  • Base-pair insertions or deletions may produce frameshift mutations
• Mutagens
  • Spontaneous mutations can occur during DNA replication, recombination, or repair
  • Chemical and physical mutagens can also alter genes

Concept 18.1- A virus has a genome but can reproduce only within a host cell

• The Discovery of Viruses: Scientific Inquiry
  • Researchers discovered viruses in the late 1800s by studying a plant disease, tobacco mosaic disease
• St ructure of Viruses
  • Small nucleic acid genome enclosed in a protein capsid and sometimes a membranous envelope containing viral proteins and help viruses end cells
  • The genome may be single or double stranded DNA or RNA
• General Features
  • Viruses use enzymes, ribosomes, and small molecules of host cells to synthesize progeny viruses
  • Each type of virus has a characteristic host range
• Reproductive Cycles of Phages
  • In the lytic cycle, entry of the viral genome into a bacterium programs destruction of host DNA, production of new phages, and digestion of the host’s cell wall, releasing the phages
  • In the lysogenic cycle, the genome of a temperate phage inserts into the daughter cells until it is induced to leave the chromosome and initiate a lytic cycle
• Reproductive Cycles of Animal Viruses
  • Many animal viruses have an envelope
  • Retroviruses (like HIV) use the enzyme reverse transcriptase to copy their RNA genome into DNA, which can be integrated into the host genome20as a provirus
• Evolution of Viruses
  • Since viruses can reproduce only within cells, they probably evolved after the first cells appeared, perhaps as packaged fragments of cellular nucleic acid

Concept 18.3- Rapid reproduction, mutation, and genetic recombination contributes to the genetic diversity of bacteria

• The Bacterial Genome and Its Replication
  • The bacterial chromosome is usually a circular DNA molecule with few associated proteins
  • Plasmids are smaller circular DNA molecules that can replicate independently of the chromosome
• Mutation and Genetic Recombination as Sources of Genetic Variation
  • Because bacteria can proliferate rapidly, new mutations can quickly increase a population’s genetic variation
  • Further diversity c an arise by recombination of the DNA from 2 different bacterial cells
• Mechanisms of Gene Transfer and Genetic Recombination in Bacteria
  • New bacterial strains can arise by the transfer of DNA from one cell to another cell
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  • In transformation, naked DNA enters the cell from the surrounding
  • In transduction, bacterial DNA is carried from one cell to another by phages
  • In conjugation, an F+ donor cell, which contains the F plasmin, transfers plasmid DNA to an F- recipient cell

The F factor of an Hfr cell, which is integrated into the bacterial chromosome, brings some chromosomal DNA along with it when it is transferred to an F- cell.

R plasmids confer resistance to various antibiotics

• Transposition of Genetic Elements
  • DNA segments that can insert at multiple sites in a cell’s DNA contribute to genetic shuffling in bacteria
  • Insertion sequence, the simplest bacterial transposable elements, consist of inverted repeats of DNA flanking a gene for transposase
  • Bacterial transposons have additional genes, such as those for antibiotic resistance

Concept 19.1- Chromatin structure is based on successive levels of DNA packing

• Nucleosomes, or “Beads on a String”
  • Eukaryotic chromatin is composed mostly of DNA and histone proteins that bind to each other and to the DNA to from nucleosomes, the most basic units of DNA packing
  • Histone tails extend outward from each bead-like nucleosome core
• Higher Levels of DNA Packing
  • Additional folding leads ultimately to the highly condensed chromatin of the metaphase chromosomes
  • In interphase cells, most chromatin is less compaced (euchromatin), but some remains highly condensed (heterochromatin)

Concept 20.2- Restriction fragment analysis detects DNA differences that affect restriction sites

• Gel Electrophosresis and Southern Blotting
  • DNA restriction fragments of different lengths can be separated by gel electrophoresis
  • Specific fragments can be identified by Southern blotting, using labeled probes that hybridize to the DNA immobilized on a “blot” of gel
• Restriction Fragment Length Differences as Genetic Markers
  • Restriction fragment length polymorphis ms (RFLPs) are differences in DNA sequence on homologous chromosomes that result in restriction fragments of different lengths, which can be detected by Southern blotting
  • The thousands of RFLPs present throughout eukaryotic DNA can serve as genetic markers

Concept 21.2- Different cell types result from differential gene expression in cells with the same DNA

• Evidence for Genomic Equivalence
  • Cells differ in structure and function not beacuse they contain different genes but because they express different portions of a common genomes; they have genomic equivalence
  • Differentiated cells from mature plants are often totipotent, capable of generating a comple new plant
  • The nucleus from a differentiated animal cell can sometimes give rise to a new animal if transplanted to an enucleated egg cell
  • Pluripotent stem cells from animal embryos or adult tissues can reproduce and differentiate in vitro as well as in vivo, offering the potential for medical use
• Transcriptional Regulation of Gene Expression During Development
  • Differentiation is=2 0healded by the appearance of tissue-specific proteins
    • These proteins enable differentiated cells to carry out their specialized roles
• Cytoplasmic Determinants and Cell-Cell Signals in Cell Differentiation
  • Cytoplasmic determinants in the cytoplasm of the unfertilized egg regulate the expression of genes in the zygote that affect the developmental fate of embryonic cells
  • In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells

Concept 21.3- Pattern formation in animals and plants results from similar genetic and cellular mechanisms

• Pattern Formation
  • The development of a spatial organization of tissues and organs, occurs continually in plants but is mostly limited to embryos and juveniles in animals
  • Positional information, the molecular cues that control pattern formation, tell a cell its location relative to the body’s axes and to other cells
• Drosophila Development: A Cascade of Gene Activations
  • After fertilization, positional informati on on an increasingly fine scale specifies the segments in Drosophila and finally triggers the formation of each segment’s characteristic structures
  • Gradients of morphogens encoded by maternal effect genes, such as bicoid, produce regional differences in the sequential expression of threes sets of segmentation genes, the products of which direct the actual formation of segments
  • Finally, master regulatory genes, called homeotic genes, specify the type of appendages and other structure that form on each segment

Transcription factors encoded by the homeotic genes are regulatory proteins the control the expression of genes responsible for specific anatomical structure

• C. elegans: The Role of Cell Signaling
  • The complete lineage of each cell in C.elegans in known
  • Cell signaling and induction are critical in determining worm cell fates, including apoptosis (programmed cell death)
  • An inducing signal produced by one cell in the embryo can initiate a chain of inductions that results in the formation of a particular organ, such as the intestine or vulva
  • In apoptosis, precisely timed signals trigger the activation of a cascade of “suicideD proteins in the cells destined to die
• Plant Development: Cell Signaling and Transcriptional Regulation
  • Induction by cell-cell signaling helps determine the number of floral organs that develop from a floral meristem
  • Organ identity genes determine the type of structure that grows from each whorl of a floral meristem
  • The organ identity genes apparently act as master regulatory genes, each controlling the activity of other genes that more directly bring about an organ’s structure and function

Concept 22.1- The Darwinian revolution challenged traditional views of a young Earth inhabited by unchanging species

• Resistance to the Idea of Evolution
  • Darwin’s theory that life’s diversity has arisen from fewer ancestral species through natural selection was a radical departure from the prevailing views of Western Culture
• Theories of Gradualism
  • Geologists Hutton and Lyell perceived that changes in Earth’s surface can result from slow, continuous actions still operating at the present time
• Lamarck’s Theory=2 0of Evolution
  • Lamarck hypothesized that species evolve, but the mechanisms he proposed are unsupported by evidence

Concept 22.2- In The Origin of Species, Darwin proposed that species change through natural selection

• Darwin’s Research
  • Darwin’s experiences during the voyage of HMS Beagle provided much of the background for his idea that new species originate from ancestral forms through the gradual accumulation of adaptations
  • After returning to England, he refined his theory and finally published it in 1859 after learning that Wallace had the same idea
• The Origin of Species
  • Darwin’s book describing his theory of descent with modification, Darwin recognized that there are heritable variations in populations and that some of those variations are better suited than others to a particular environment
  • Because organisms tend to produce many more offspring than the environment can support, there is competition for resources, and those that are better suited to the environment tend to have greater success in surviving and reproducing

Thus, these better-suited individuals leave more offspring than other individuals

• Over time, this process of natural selection can result in adaptation of organisms to their environment

Concept 22.3- Darwin’s theory explains a wide range of observations

• Natural Selection in Action
  • Researchers have observed natural selection leading to adaptive evolution in wild guppy populations
  • In humans, the use of drugs selects for pathogens that through chance mutations are resistant to the drugs’ effects
  • The ability of bacteria and viruses to evolve rapidly poses a challenge to our society
• Homology, Biogeography, and the Fossil Record
  • Evolutionary theory explains many kinds of observations, including structural and molecular similarities, geographic distribution of organisms, and the fossil record
• What Is Theoretical about the Darwinian View of Life?
  • Darwin’s theory of evolution by natural selection integrates diverse areas of biological study and stimulates many new research questions
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Concept 23.1 (10 questions)- Population genetics provides a foundation for studying evolution

• The Modern Synthesis
  • The modern synthesis integrates Mendelian genetics with the Darwinian theory of evolution by natural selection and focuses on populations as the basic unit of evolution
• Gene Pools and Allele Frequencies
  • A population, a localized group of organisms that all belong to the same species, is united by its gene pool, the aggregate of all alleles in the population
• The Hardy-Weinberg Theorem
  • States that the frequencies of alleles and genotypes in a population will remain constant if Mendelian segregation and random mating are the only processes that affect the gene pool
  • p^2+ 2pq + q^2 = 1
  • p + q= 1

Concept 25.2- Phylogenetic systematics connects classification with evolutionary history

• Binomial Nomenclature
  • Linnaeus’s system gives organisms two-part names: a=2 0genus plus a specific epithet
• Hierarchical Classification
  • Linnaeus introduced a system for grouping species in increasingly broad categories
• Linking Classification and Phylogeny
  • Systematists depict evolutionary relationships as branching phylogenetic trees, which may be based on various kinds of evidence

Concept 25.3- Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters

• Cladistics
  • A clade is a monophyletic grouping of species that includes an ancestral species and all its descendants
  • In cladistic analysis, clades are defined by their evolutionary novelties, or shared derived characters
  • These are identified by comparing ingroup species with an outgroup species that does not have the shared derived character
• Phylogenetic Trees and Timing
  • In phylograms, the length of a branch reflects the number of evolutionary changes in the lineage
  • Ultrametric trees place evolut ionary brach points in the context of geologic time
• Maximum Parsimony and Maximum Likelihood
  • Among phylogenetic hypotheses, the most parsimonious tree is the one that requires the fewest evolutionary changes, and the most likely tree is the one based on the most likely pattern of changes
• Phylogenetic Trees as Hypotheses
  • The best phylogenetic hypotheses are those that are consistent with the most data: morphological, molecular, and fossil

Concept 25.4- Much of an organism’s evolutionary history is documented in its genome

• Gene Duplications and Gene Families
  • Orthologous genes, found in a single copy in the genome, can diverge only after speciation has taken place
  • Paralogous genes arise through duplication with a genome and can diverge within a clade, often adding new functions
• Genome Evolution
  • Orthologous genes are often shared by distantly related species
  • The relatively small variation in total gene number in organisms of varying comple xity indicates that genes in complex organisms are extremely versatile and that each gene can perform many functions

Concept 26.3- As prokaryotes evolved, they exploited and changed young Earth

• The First Prokaryotes
  • Prokaryotes were Earth’s sole inhabitants from 3.5 to about 2 billion years ago
• Electron Transport Systems
  • The first electron transport chains may have saved ATP by coupling the oxidation of organic acids to the transport of H+ out of the cell
• Photosynthesis and the Oxygen Revolution
  • The earliest types of photosynthesis did not produce oxygen
  • Oxygenic photosynthesis probably evolved about 3.5 billion years ago in cyanobacteria
  • The accumulation of oxygen in the atmostphere about 2.7 billion years ago posed a challenge for life, but it also selected for certain adaptations such as cellular respieration using oxygen

Concept 27.1- Structural, functional, and genetic adaptations contribute to prokaryotic success

• Cell-Surface Structures
  • Nearly all prokaryotes have a cell wall
  • Gram-positive and gram-negative bacteria differ in the structure of their walls
  • Many species have a capsule, fimbriae, and pili outside the cell wall, which help the cells adhere to one another or to a substrate
• Motility
  • Most motile bacteria propel themselves by flagella, which are structurally and functionally different from eukaryotic flagella
  • In heterogeneous environment, many prokaryotes can move forward or away from certain stimuli
• Internal and Genomic Organization
  • Prokaryotic cells usually lack complex compartmentalization
  • The typical prokaryotic genome is a ring of DNA that is not surrounded by a membrane
  • Some species also have smaller rings of DNA called plasmids
• Reproduction and Adaptation
  • Prokaryotes reproduce quickly by binary fission
  • Many form endospores which can remain viable in harsh conditions for centurie s
  • Rapid reproduction and horizontal gene transfer facilitate the evolution of prokaryotes in changing environments

Concept 27.2- A great diversity of nutritional and metabolic adaptations have evolved in prokaryotes

• Four Modes of Nuitrition
  • Photoautotrophy, chemoautotrophy, photoheterotrophy, and chemoheterotrophy are found among prokaryotes
• Metabolic Relationships to Oxygen
  • Obligate aerobes require O2, obligate anaerobes are poisoned by 02, and facultative anaerobes can survive with or without 02
• Nitrogen Metabolism
  • Prokaryotes can metabolize a wide variety of nitrogenous compounds
  • Some can convert atmospheric nitrogen to ammonia in a process called nitrogen fixation
• Metabolic Cooperation
  • Many prokaryotes depend on the metabolic activites of other prokaryotes
  • In cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells exchange metabolic products
  • Some prokar yotes can form surface-coating colonies called biofilms, which may include different species

Concept 27.3- Molecular systematics is illuminating prokaryotic phylogeny

• Lessons from Molecular Systematics
  • Molecular systematics is leading to a phylogenetic classification of prokaryotes, allowing systematists to identify major new clades
• Bacteria
  • Diverse nutritional types are scattered among the major groups of bacteria
  • The two largest groups are proteobacteria and the gram-positive bacteria
• Archaea
  • Archaea share certain traits with bacteria and other traits with eukaryotes
  • Some archaea share certain traits with bacteria and other traits with eukaryotes
  • Some archaea live in extreme environment
    • Extreme thermophiles, extreme halophiles, and methanogens

Concept 27.5- Prokaryotes have both harmful and beneficial impacts on humans

• Pathogenic20Prokaryotes
  • Typically cause disease by releasing exotoxins or endotoxins and are potential weapons of bioterrorism
  • Horizontal gene transfer can spread genes associated with virulence to harmless strains
• Prokaryotes in Research and Technology
  • Experiment involving prokaryotes such as E. coli and A. tumefaciens have led to important advances in DNA technology
  • Prokaryotes are major tools in bioremediation, mining, and the synthesis of vitamins, antibiotics, and other products

Concept 28.1- Protists are an extremely diverse assortment of eukaryotes

• Protist Diversity
  • More diverse than all other eukaryotes and are no longer classified in a single kingdom
  • Most protists are unicellular while some are colonial or multicellular
  • Potists include photoautotrophs, heterotrophs, and mixotrophs
  • Most are aquatic but others are found in moist terrestrial habitats
  • Some speices are asexual while others reproduce sexually
• Endosymbiosis in Eukaryotic Evolution
  • Some biologists hypothesize that mitochondria and plastids are descendants of alpha proteobacteria and cyanobacteria, respectively, that were engulfed by other cells and became endosymbionts
  • The plastid-bearing lineage eventually evolved into red algae and green algae
  • Other protist groups evolved from secondary endosymbiotic events in which red algae or green algae were themselves engulfed

Concept 28.4- Alveolates have sacs beneath the plasma membrane

• Alveoli
  • Membrane-bounded sacs beneath the plasma membrane, distinguish alveolates from other protists
• Dinflagellates
  • Diverse group of aquatic photoautotrophs and heterotrophs
  • Their characteristic spinning movements are produced by 2 flagella that lie in perpendicular grooves in their cell surface
  • Rapid growth of some dinoflagellate populations causes red tides
• Apicomplexans
  • Parasites that have an apical c omplex of organelles specialized for invading host cells
  • Have a nonphotosynthetic plastic, the apicoplast
  • Type can cause malaria
• Ciliates
  • Use cilia to move and feed
  • Have large macronuclei and small micronuclei
  • The micronuclei function during conjugation, a sexual process that produces genetic variation
    • Conjugation is separate from reproduction which generally occurs by binary fission

Concept 28.5- Stramenopiles have “hairy” and smooth flagella

• Oomycetes
  • Most are decomposers or parasites and have filaments (hyphae) that facilitate nutrient uptake
  • Type can cause potato late blight
• Diatoms
  • Surrounded by a two part glass-like wall and are a major component of phytoplankton
  • Accumulations of fossilized diatom walls comprise much of the sediments known as diatomaceous earth
• Golden Algae
  • Typically have 2 flagella attached near one end of the cell
  • Many species are planktonic
  • Their color results from the carotenoids they contain
• Brown Algae
  • Multicellular, mostly marine protists that include some of the most complex algae commonly known as seaweeds, many of which are commercially important to humans
  • Like some red algae, green algae, and all plants, some brown algae have a life cycle that features alternation of generations
    • Multicellular diploid form alternates with a multicellular haploid form

Concept 32.1- Animals are multicellular, heterotrophic eukaryotes with tissues that develop from embryonic layers

• Nutritional Mode
  • Animals are heterotrophs that ingest their food
• Cell Structure and Specialization
  • Animals are multicellular eukaryotes
  • Cells lack cell walls
  • Bodies held together instead by structural proteins such as collagen
  • Nervous tissue and muscle tissue are unique to animals
• Reproduction and Development
  • Gastrulation follows the formation of the blastula, resulting in formation of embryonic tissue layers
  • All animals have Hox genes that regulate the development of body form
  • Although the Hox family of genes has been highly conserved, it can produce a wide diversity of animal morphology

Concept 32.3- Animals can be characterized by “body plans”

• Symmetry
  • Animals may lack any symmetry or have radial or bilateral symmetry
  • Bilaterally symmetrical animals have dorsal and ventral sides, as wall as anterior and posterior ends
  • Many bilaterally symmetrical animals have undergone cephalization
• Tissues
  • Animal embryos form germ layers and may be diploblastic (have 2 germ layers) or tripolblastic
• Body Cavities
  • In triploblastic animals, a body cavity may be present of abset
  • A body cavity can be a psuedocoelom or a true coelom
• Protostome and Deuterostome Development
  • These two modes of development differ in characteristics of cleavage, coelom formation, and blastopore fate

Concept 33.1- Sponges are sessile have have a porous body and choanocytes

• See Table 33.7.
• Sponges
  • Lack true tissues and organs
  • Suspension feed by drawing water through pores; choanocytes (flagellated collar cells) ingest suspended food

Concept 33.2- Cnidarians have a radial symmetry, a gastrovascular cavity, and cnidocytes

• Cnidarians
  • Mainly marine carnivores possessing tentacles armed with cnidocytes that aid in defense and the capture of prey
  • Two body forms are sessile polyps and floating medusae
• Hydrozoans
  • Class that usually alternated polyp and medusa forms, although the polyp is more conspicuous
• Scyphozoans
  • Class where jellies (medusae) are the prevalent form of life cycle
• Cubozoans
  • Class with box jellies and sea wasps, the medusa is box-shaped and has complex eyes
• Anthozoans
  • Class that contains the sea anemones and corals, which occur only as polyps

Concept 33.3- Most animals have bilateral symmetry

• Flatworms
  • Dorsoventrally flattened animals with a gastrovascular cavity
  • Class Tuberbellara is made up of mostly free-living, primarily marine species
  • Classes Trematoda and Monogenea live as parasites in or on animals
  • Class Cestoda consists of tapeworms, all of which are parasite and lack a digestive tract
• Rotifers
  • Found mainly in fresh water, many rotifer species are parthenogenetic
• Lophophorates: Ectoprocts, Phoronids, and Brachiopods
  • Lophophorates are coelomates that have a lophopore, a horseshoe-shaped, suspension-feeding organ bearing ciliated tentacles
• Nemerteans
  • Have a unique retractable tube (proboscis) used for defense and prey capture
  • A fluid-filled sac is used to extend the proboscis

Concept 33.7- Arthropods are segmented coelomates that have an exoskeleton and jointed appendages

• General Characteristics of Arthropods
  • Variation in arthropod morphology consists mainly in specializations of groups of segments and in appendages
  • The arthropod exoskeleton, make of protein and chitin, undergoes regular ecdysis (molting)
• Cheliceriforms
  • Include spinders, ticks, and mites
  • Have an anterior cephalothorax and a posterior abdomen
  • The most anterior appendages are=2 0modified as chelicerae (either pincers or fangs)
• Myriapods
  • Millipedes are wormlike, with a large number of walking legs
  • Among the first animals to live on land
  • Centipedes are terrestrial carnivores with poison claws
• Insects
  • Exceed all other animal combined in species diversity
  • Flight has been an important factor in the success of insects
• Crustaceans
  • Include lobsters, crabs, shrimp, and barnacles, and primarily aquatic
  • Have numerous appendages, many of which are specialized for feeding and locomotion

Concept 33.8- Echinoderms and chordates are deuterosomes

• Echinoderms
  • Sea stars and their relatives have a water vascular system ending in tube feet used for locomotion and feeding
  • The radial anatomy of many species evolved secondarily from the bilateral symmetry of ancestors
  • A thin, bumpy, or spiny skin covers a calcareous endoskeleton
• Chordates
  • Include two invertebrate subphyla and all vertebrates
  • Share many features of embryonic development with echinoderms

Concept 34.1- Chordates have a notochord and a dorsal, hollow nerve cord

• Derived Characters of Chordates
  • Include a notochord; a dorsal, hollow nerve cord; pharyngeals slits of clefts; and muscular, post-anal tail
• Tunicates
  • Marine suspension feeders commonly called sea squirts
  • Lose some of the derived characters of chordates as adults
• Lancelets
  • Marine suspension feeders that retain the hallmarks of the chordate body plan as adults
• Early Chordate Evolution
  • Current life history of tunicates probably does not reflect that of the ancestral chordate
  • Gene expression in lancelets holds clues to the evolution of the vertebrate brain

Concept 34.4- Gnathostomes are vertebrates that have jaws

• Derived Characters of Gnathostomes
  • Have jaws, which evolved from skeletal supports of the pharyngeal slits; enhanced sensory systems, including the lateral line system; an extensively mineralized endoskeleton, and pair appendages
• Fossil Gnathostomes
  • Placoderms were close relative of living gnathostomes
  • Acanthodians were closely related to osteichthyans
• Chondrichthyans (Sharks, Rays, and Their Relatives)
  • Have a cartilaginous skeleton that evolved secondarily from an ancestral mineralized skeleton
• Ray-Finned Fishes and Lobe-Fins
  • Osteichthyans have a skeleton reinforced by calcium phosphate
  • Aquatic formshave bony gill covers and a swim bladder; some also have lungs
  • Ray-finned fishes have maneuverable fins supported by long rays
  • Lobe-fins include coelacanths, lungfish es, and tetrapods
  • Aquatic lob-fins have muscular pectoral and pelvic fins

Concept 34.7- Mammals are amniotes that have hair and produce milk

• Derived Characters of Mammals
  • Hair and mammary glands are 2 derived characteristics of mammals
• Early Evolution of Mammals
  • Evolved from synapsids in the late Triassic period
  • Living lineages of mammals originated in the Jurassic but did not undergo a significant adaptive radiation until the beginning of the Paleogene
• Monotremes
  • A small group of egg-laying mammals consisting of echidnas and the platypus
• Marsupials
  • Opossums, kangaroos, and koalas
  • Young begin their embryonic development attached to placenta in the mother’s uterus but complete development inside a maternal pouch
• Eutherians (Placental Mammals)
  • Eutherians have young that complete their em bryonic development attached to a placenta
  • All primates have hands and feet adapted for gripping
  • Living primates include lemurs and their relatives, taisers, and anthropoids
  • Anthropoids diverged early into New World and Old World monkeys
  • Hominoids (gibbons, orangutans, gorillas, chimpanzees, bonobos, and humans) evolved from Old World monkeys

JSleigh, 1/2/08, adapted from Carolina Biological pBLU Transformation.