LATEST SECTION (pg 17 begins brief review of total semester’s topics) ????
Ch. 23 & 35 VIRUSES / IMMUNE SYSTEM In broad and general terms, describe how HIV infects host cells (23.8.1 - pgs 513-514)
-HIV has a glycoprotein (gp120) on its surface that fits the cell-surface marker protein CD4 on the surfaces of the immune system macrophages and T cells. Then, a coreceptor pulls the HIV across the cell membrane. After gp120 binds to CD4, it goes through a conformational change that allows it to bind the coreceptor. Once in the host cell, the HIV particle sheds its protective cote, leaving viral RNA floating in the cytoplasm with reverse transcriptase, which synthesizes a double strand of DNA complementary to the virus RNA, often making mistakes and introducing mutations. The double stranded DNA enters the nucleus along with a viral enzyme that incorporates the viral DNA into the host cell’s DNA.
explain the difference between antigenic drift and antigenic shift (23.8.2 - slide #11)
-Antigenic drift is the result of an accumulation of mutations of genes while antigenic shift is the result of a recombination of novel H and N combinations. Additionally, only an antigenic shift can cause a pandemic.
define pandemic and describe the 3 conditions necessary for a pandemic (slide #11)
-pandemic: an epidemic of an infectious disease that has spread through human populations across a large region (cannot happen in a single city/state) If you want to learn more check out cosc 175 towson
1. New strain must contain a novel H & N combination
2. Must be able to replicate in humans
3. Must be efficiently transmitted between humans
Describe the two broad types of immunity (slide #12) -innate: based on recognition of pathogens (initial responder, fast) - more general
Don't forget about the age old question of ∙ The presence of pillow lava is evidence of what volcanic circumstance?
-adaptive: based on antigen recognition, reacts by memory (production of immune cells = cellular; production of antibodies = humoral) - more specific We also discuss several other topics like general physics study guide
Describe the function of pattern recognition receptors (35.8.1 - slide #13)
-Pattern recognition receptors are receptors to molecules that pathogens cannot change.
-toll-like receptor: some recognize extracellular pathogen molecules (bacterial glycoproteins); some recognize intracellular pathogen molecules (viral DNA & RNA)
Describe the inflammatory response (35.8.2 - slide #16) 1. Injured cells release chemical alarms
2. Cause vasodilation (redness) and increased permeability (edema) 3. Phagocytes accumulate at the site
4. Pain due to nerve irritation and swelling
5. Elevated body temp (enhances phagocytic activity, inhibits pathogen growth)
Describe the characteristics of adaptive immunity (35.8.3) 1. Recognize specific antigens
2. Recognize diverse antigens
3. Have memory, causing quicker response to second exposure 4. Can distinguish self from non-self (antigen)
Explain the roles of major histocompatibility (MHC) classes I and II (35.9.1 - pg 844) We also discuss several other topics like rls 300 class notes
• Self markers
• MHC I are present on every nucleated cell of the body and cause a response in Tc cells
• MHC II are present only on antigen-presenting proteins (macrophages, B cells, and dendritic cells) and cause a response in TH cells
Describe the function of cytotoxic T (Tc) cells (35.9.1 - slide #19) • Recognize “altered self” bound to MHC I and induce apoptosis; express CD8 co-receptor; recognize intracellular antigens
Explain the role of helper T (TH) cells (35.9.2 - slide #19) • Respond to peptides bound to MHC Class II proteins Don't forget about the age old question of radford gis
Describe how antigen is recognized by antibodies (pgs 845-846) • Antigens provoke a specific immune response. The greater the “foreignness” of an organism, the greater the immune response. Two types of immunity fight off antigens: cell-mediated immunity and humoral immunity.
Differentiate between cell-mediated immunity and humoral immunity (slides 21 & 22)
• CD8+ Tc cells: induce apoptosis of “altered self” cells
• Naive Tc cells activated by TCR and CD8 binding of
peptides bound to MHC Class I
• Activated Tc cells expand clonally
• Produce Tc cells that circulate
• Produce memory Tc for rapid second exposure
• CD4+ cells (exogenous antigens)
• Activated by TCR and CD4 binding of peptides bound to MHC class II
• Secrete cytokines that activate or differentiate (help) other immune cells
• Activated Th cells expand clonally Don't forget about the age old question of uhd math
• Effector & memory cells
• Recognize antigen with antibodies (immunoglobulins)
• Produce antibodies for cell surface
• Produce & secrete soluble antibodies for the circulation
• Ig each with 2 light chains and 2 heavy chains (with 5 different sequences → IgA, IgD, IgE, IgG, IgM)
• Antigen specificity in variable region
• Naive B cells encounter antigen in lymph organs
• Antibody binds antigen
• B cell receives signals from Th cells
• B cell is activated
• B cell proliferation
• Memory cells
• Plasma cells that produce soluble antibodies
explain how vaccination prevents disease (35.10.3)
• Vaccinations give antibodies an exposure to the antigen in a naive form to elicit an initial (primary) response. The symptoms develop, clonal expansion of T & B cells occur, secretion of Ig begins, and
memory cells develop. This allows, in the event that the body comes into contact with the real disease, the antibodies to react much quicker in the second exposure due to the memory cells.
Ch. 36 & 10 STEM CELLS / CLONING / CANCER Define cellular potency (slide 2) and differentiate between totipotent and pluripotent
• Cell potency: the ability to differentiate into other cell types • Totipotent cells are able to differentiate into all other cell types while pluripotent can differentiate into all except one and is divisible into any of 3 germ layers, endoderm, mesoderm, ectoderm
Differentiate between reproductive and therapeutic cloning • Reproductive cloning - SCNT used to make an animal genetically identical to another, the embryo is placed into a uterine environment, success rate is low, age-associated diseases, lack of imprinting (insufficient time to chromatin remodeling, insufficient time for reprogramming)
• Therapeutic cloning - SCNT used to create an embryo, cloned cells cells remain in a dish in the lab, used to replace damaged organs not implanted into a female uterus, solves the problem of immune rejection
Describe how nuclear reprogramming can be used for therapeutic cloning (36.5.2&36.5.3, & slide 8)
• Nuclear reprogramming: a nucleus from a differentiated cell undergoes epigenetic changes that must be reversed to allow the nucleus to direct development
• Epigenetic changes: heritable changes in gene expression that occur without changes to DNA sequences, often via methylation of DNA, and a variety of modification to histone proteins
• In therapeutic cloning, somatic cell nuclear transfer (SCNT) is used to create an embryo.
Describe the characteristics of cancer
1. Failure of cell cycle control causes excessive proliferation 2. Loss of contact inhibition
3. Lack of adhesiveness
4. immature/relatively undifferentiated cells
5. Promotion of angiogenesis
Describe cancer in terms of changes in cell cycle control (10.7.1) Cancer loses the tumor suppression gene, therefore, no apoptosis is present and the cells replicate and clone uncontrollably.
Ch. 19 POPULATION GENETICS
Differentiate between evolution by natural selection and the inheritance of acquired characteristics. 19.1.1
• Natural selection: the most favorable variant alleles are passed on to the next generation, leading to evolutionary change
• Acquired characteristics: changes that the individuals acquired during their lives were passed on to their offspring (short-necked giraffes stretched their necks to feed on tree leaves, leading to the long necked giraffes)
Define fundamental aspects and terminology of population genetics. 19.1.2
• PG: study of gene frequencies in a population
• Evolution results in a change in the genetic composition of a population
• Genetic variation is the raw material for evolutionary change • Human population genetic variation: genes that influence blood groups; genes that influence enzymes
• Polymorphic variation: more than one allele at a locus
Describe the characteristics of Hardy-Weinberg equilibrium. 19.2.1, 19.2.2
Proportions of genotypes do not change if:
1. No mutation takes place
2. No genes are transferred to or from other sources (no immigration or emigration)
3. Random mating is occurring
4. The population size is very large
5. No selection occurs
Describe how mutation, gene flow, nonrandom mating, and genetic drift can cause evolutionary change. 19.3.1, 19.3.2, 19.3.3, 19.3.4 • Mutation: mutation is the ultimate source of variation; individual mutations occur so rarely that mutation alone usually does not change allele frequency much
• Gene flow: very potent agent of change; individuals or gametes move from one population to another
• Nonrandom mating: inbreeding is the most common form; it does not alter allele frequency but reduces the proportion of heterozygotes • Genetic drift: statistical accidents; the random fluctuation in allele frequencies increases as population size decreases
Describe how selection can cause evolutionary change. 19.3.5 • Artificial selection: a breeder selects for desired traits
• Natural selection: environmental conditions determine which individuals in a population produce most offspring
• Natural selection can be driven by selection to avoid predation, to match climate conditions, and to resist pesticides and microbes to increase survival.
Describe the evolutionary outcomes of disruptive, directional, and stabilizing selection. 19.4.1, 19.4.2, 19.4.3
• Disruptive: acts to eliminate intermediates (beak sizes on African black-bellied seedcracker finches)
• Directional: acts to eliminate one extreme, often occurs in nature when environment changes (Drosophila, artificial selection for flies that moved away from the light)
• Stabilizing: acts to eliminate both extremes, makes intermediate by eliminating both extremes (infants in intermediate weight have highest survival rate)
Interpret how field and laboratory studies demonstrate natural selection in guppies. 19.5.1, 19.5.2
Guppies found above waterfalls are more colorful and hunted less while guppies below waterfalls are duller in color and suffer more from predation. Even when mechanically separated by scientists, the same results occurred. Thus, the conclusion that less predation causes more vibrancy of colors on the guppies was supported.
Describe fitness and its effect on natural selection and adaptation. 19.6.1, 19.6.2 (pg 421)
• Fitness: the degree to which a phenotype produces offspring (reproductive success)
• Even if no differences in survival occur, selection may operate if some individuals are more successful than others in attracting mates (sexual selection). The most fit phenotype is the one with the most reproductive success, thus increasing frequency. Natural selection and adaptation are based upon survival success, directly relating to reproductive success, i.e. fitness.
Discuss how oscillating selection and heterozygote advantage can affect population genetics. 19.7.4, 19.7.5
• Oscillating selection: selection favors one phenotype at a time and another phenotype at another time, effect will be to maintain genetic variation in the population (beak length in Galapagos)
• Heterozygote advantage: heterozygotes favored over homozygotes, works to maintain both alleles in the population (sickle cell anemia)
Ch. 17 BIOTECHNOLOGY
Define recombinant DNA and explain how restriction endonucleases produce DNA fragments with “sticky ends” (17.1.1, pg 359) • Recombinant DNA: DNA molecules formed by lab methods to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological organisms
• Restriction endonucleases cleave the phosphodiester bond within a polynucleotide chain then recognize specific sequences called restriction sites, producing staggered cuts (sticky ends).
Describe how DNA restriction fragments are joined together (17.1.2, pg 359)
• DNA ligase catalyzes the formation of a phosphodiester bond between 2 adjacent phosphate and hydroxyl groups of DNA nucleotides. The action of ligase is to seal nicks in one or both strands.
Describe how restriction enzymes and RFLP (restriction fragment length polymorphisms) can be used to determine paternity or identify individuals at a crime scene
• The DNA sequences fragmented by restriction enzymes and RFLP (mutations that change DNA sequences and can eliminate sequences recognized) allow the identification of specific DNA sequences to compare and match in paternity and evidence at a crime scene.
Describe how vectors are used in molecular cloning (17.2.1, slide 8) • Cloning of large sequences involves the production of rDNA in cells, and a vector carries the rDNA that can replicate in the host.
Describe what elements must be present in a plasmid vector (17.2.1, pg 362)
• Plasmid vectors must have an origin of replication, a selectable marker (usually antibiotic resistant), and one or more unique restriction sites where foreign DNA can be added.
Compare genomic and cDNA libraries (slide #11)
• Genomic library: collection of total genomic DNA in single organism • Isolate organism’s DNA, fragment DNA (introns and exons), insert fragments into cloning vectors
• cDNA library: combo of complementary DNA fragments inserted into host cell
• Makes cDNA from mRNA (meaning expressed genes only, NO INTRONS) using reverse transcriptase, ssDNA converted to dsDNA, used to reproduce eukaryotic genomes
Describe how the polymerase chain reaction can amplify DNA sequences (17.3.3, pg 371 and slide #12)
• PCR uses primers cyclically on specific sequences of DNA, producing large amounts. The stages include denaturation, annealing, and extension (DNA synthesis).
Describe three applications of molecular cloning technology (17.4.1, pgs 373-374 and slide #15)
• Expression vectors allow production of specific gene products • Contain sequences necessary to drive expression of inserted DNA in a specific cell type, namely the correct sequences to permit transcription and translation of the sequences
• EX. Human recombinant insulin
• Genes can be introduced across species barriers
• Gene insertion without reproduction → transgenic
• EX. Eyeless gene in Drosophila
• Cloned genes can be used to construct “knockout” mice • Replace the “wild type” gene with the mutated gene, impact is assessed in adult mice
Describe the potential problems of gene therapy (17.5.3) • Genes must be targeted to the right tissue and genes must be regulated normally for therapy to work properly
Describe the pros and cons of genetically modified organisms (GMOs) (see the examples in 17.6.2 and 17.6.4)
• greater crop yields will feed more people
• More economical (needs less herbicide, pesticide, and man power for production)
• Improved quality (fresher longer)
• Resistance to weather fluctuations (drought, frost, and flood resistant)
• Engineered to have a high content of a specific nutrient (golden rice and beta carotene)
• Phytoremediation: engineered plants grown on contaminated soil to remove contaminants (gas works park in seattle)
• allergies in humans
• genetic flow into wild crops (cross pollination, lower biodiversity) • Resistance in target organisms (weeds, etc)
• Emergence of new diseases
Ch. 20 EVIDENCE WITH EVOLUTION
Explain how evolutionary change has occurred in Darwin’s finches. 20.1.1, 20.1.2, 20.1.3
• In seasons of drought, birds with deeper and more powerful beaks survived better while in seasons of normal rainfall, the average beak size returned to its original size
Explain how selection has shaped patterns of evolutionary change in peppered moths. 20.2.1
• The closer the moth color was to the bark, the less predation. During periods of higher pollution, darker moths increased in frequency because they blended in with the bark. When measures were taken to lower pollution and bark lightened, lighter moths regained frequency in the population.
Compare and contrast natural and artificial selection. 20.3.1 (slide #18)
• Natural selection:
• Artificial selection: change initiated by humans, operates by favoring individuals with certain phenotypic traits, allowing them to reproduce and pass their genes on to the next generation
• Both result in evolutionary change, but natural selection is the main process for evolution, and artificial selection can lead to a more rapid change.
Explain the importance of transitional fossils. 20.4.1, 20.4.2 • Transitional fossils help fill in evolutionary gaps, such as the Archaeopteryx (intermediate between bird and dinosaur, exhibits ancestral traits as well as traits found in the present day bird).
Explain the evolutionary significance of homologous structures. 20.5.1, 20.5.2
• Homologous structures, structures with different functions and appearances but stem from the same body part, provide evidence that we all derived from a common ancestor.
Explain the evolutionary significance of vestigial structures. 20.5.4 • Vestigial structures, structures that exist in an organism that no longer serve a purpose but do not exhibit any dangerous effects either, prove evolution occurs because those structures must have served a purpose at one time.
Describe how genetic evidence can demonstrate evolutionary relationships. 20.6.1
• Phylogenetic trees demonstrate genetic evidence as it demonstrates common ancestors. New alleles arise from older ones. Distantly related organisms accumulate a greater number of evolutionary differences. Divergence can be seen at the protein level.
Explain the principle of convergent evolution. 20.7.1
• Convergent evolution: similar forms having evolved in different areas because of similar selective pressures in similar environments (EX. marsupials in Australia resembling placental mammals on other continents).
Ch. 21 SPECIATION
Explain the biological species concept and discuss its shortcomings. 21.1.1, 21.1.4
• Biological species concept
• Accounts for distinctiveness of species that occur together at a single locality and the connection that exists among different populations belonging to the same species
• Groups of actually or potentially interbreeding natural
populations which are reproductively isolated from other such groups
• Species composed of populations whose members mate with each other and produce fertile offspring
• Reproductive isolation - do not mate with each other or do not produce fertile offspring
• Focuses on ability to exchange genes
• Reproductive isolation may not be the only force maintaining species integrity
• Interspecific hybridization (50% of California plant species not well defined by genetic isolation → syngameon; 10% of bird species known to hybridize in nature)
• Asexual reproduction
Distinguish among the different forms of prezygotic and postzygotic isolating mechanisms. 21.1.2, 21.1.3
• Prezygotic isolating mechanisms
• Ecological isolation: species occur in the same area but they occupy different habitats and rarely encounter each other
• Behavioral isolation: species differ in their mating rituals • Temporal isolation: species reproduce in different seasons or at different times of the day
• Mechanical isolation: structural differences between species prevent mating
• Prevention of gamete fusion: gametes of one species function poorly with the gametes of another species or within the
reproductive tract of another species
• Postzygotic isolating mechanisms
• Hybrid inviability or infertility: hybrid embryos do not develop properly; hybrid adults do not survive in nature or hybrid adults are sterile or have reduced fertility
Explain how and why natural selection can reinforce reproductive isolation. 21.2.1
• Two populations may only be partially reproductively isolated. In some cases, initially incomplete isolating mechanisms are reinforced by natural selection until they are completely different.
Explain how allopatric speciation occurs. 21.4.1
• A continuous population becomes separated into two locations, producing 2 new populations.
Explain how parapatric speciation occurs.
• Species are in one location; attainment of reproductive isolation between populations that are continuously distributed in space, such that there is gene flow between them
Explain how sympatric speciation occurs. 21.4.2
• Species are in the same place, divergence leading to speciation occurs in the presence of substantial gene flow
Discuss how adaptive radiation can occur. 21.5.1, 21.5.3 • Adaptive radiation occurs on in environments with a small number of species but large number of resources
Ch. 1 Science of Biology
1. Describe the fundamental properties of life. 1.2.1* – Cellular organization: all composed of one or more cells – Energy utilization: all use energy
– Homeostasis: all maintain relatively constant internal conditions – Growth, development, and reproduction: all grow and reproduce – Heredity: all posses a genetic system that is based on replication and duplication of DNA
2. Describe the hierarchical nature of living systems. 1.2.2 – CELLULAR: 1. Atoms 2. Molecules 3. Macromolecule 4. Organelle 5. Cell
– ORGANISMAL: 6. Tissue 7. Organ 8. Organ System 9. Organism
– POPULATIONAL: 10. Population 11. Species 12. Community 13. Ecosystem 14. Biosphere
3. Explain emergent properties and give some examples. 1.2.3 • Emergent properties: properties that result from the way components interact
o EX. Metabolism, consciousness in brain
4. Distinguish between descriptive and hypothesis-driven science. 1.3
– Descriptive: observations lead to hypothesis, deductive reasoning o EX. Study of biodiversity
– Hypothesis-driven: suggested explanation that accounts for observation is tested experimentally, inductive reasoning
5. Distinguish between a hypothesis and scientific theory. 1.3 – Hypothesis: suggested explanation that accounts for scientific observation
– Scientific theory: deductive form – proposed explanation for natural phenomenon based on general principles; inductive form – body of interconnected concepts supported by inductive scientific reasoning and experimental evidence
6. Describe Darwin’s theory of evolution by natural selection. 1.4.3 – Evolution’s primary mechanism is natural selection, i.e. the survival of the most beneficial traits, leading to adaptations and an overall shift in species.
7. Distinguish between artificial and natural selection. 1.4.3 – Essentially, artificial selection in man-made while natural selection is a result of survival fitness.
8. Identify the major types of evidence supporting evolution and phylogenetic trees. 1.4.4
– Fossil record: transitional forms, microscopic fossils, and fossils overall give evidence for evolution from simple to complex organisms – Comparative anatomy: homologus (same evolutionary origin with different structure and function in present day) and analogous (similar function but different origins) provide evidence
– Molecular evidence: comparing genomes of different groups of animals or plants
9. Explain how evolution accounts for both the unity and diversity of life. 1.5.1
– The underlying unity of biochemistry and genetics that all life has evolved from the same origin event. The diversity we see today has arisen by evolutionary change, visible in fossil record. The retention of certain characteristics shared by all organisms, such as DNA being the storage for hereditary info, supoorts a long line of descent from a common origin.
10. Describe the three domains of life. 22.5.1
– Domain archaea: arachaea
– Domain bacteria: bacteria
– Domain eukarya: eukaryotes – includes Kingdom Plantae, Kingdom Fungi, Kingdom Animalia, and Protists (not a kingdom)
Ch. 2 Molecules and Water
1. Describe the general structure of atoms and the properties of their constituent particles. 2.1.1
– Atoms: central nucleus containing cluster of neutrons and protons with electron cloud surrounding
– Proton: positive subatomic particle
– Neutron: neutral subatomic particle
– Electron: negative subatomic particle
2. Distinguish between essential elements and trace elements. 2.2.1 – Essential elements: needed in significant amounts order to live healthy life, a deficiency causes abnormal development or functioning – Trace elements: needed in amounts <.01%
3. Identify the four most common elements in organic molecules. 2.2.1
CHON (carbon, hydrogen, oxygen, nitrogen)
4. Distinguish between covalent bonds, ionic bonds, hydrogen bonds, van der Waal’s attractions, and hydrophobic interactions. Rank these bonds/interactions based on their relative strength. 2.3.1- 2.3.4 MOST TO LEAST STRONG:
1. Covalent bonds: sharing of electrons
2. Ionic bond: attraction of opposite charges, non-directional 3. Hydrogen bonds: sharing of hydrogen atom, highly directional (attraction of opposite partial electric charges)
4. Hydrophobic interaction: forcing of hydrophobic portions of molecules together in presence of polar substances
5. van der Waals: weak attraction between atoms due to oppositely polarized electron clouds
5. Distinguish between atoms, ions, and molecules. 2.3 – Atoms: building blocks of matter/molecules
– Ions: charged molecules
– Molecules: group of atoms held together in a stable state
6. Explain the concept of electronegativity and identify the common electronegative atoms involved in polar covalent bonds in biological molecules. 2.3.2
– Electronegativity: affinity for electrons (increase L-R across periodic table and decrease going down)
– O – 3.5; N – 3.0; C – 2.5; H – 2.1
7. Distinguish between polar and nonpolar molecules. 2.3.2 – Polar molecules: regions of partial negative charge near the more electronegative atom and regions of partial positive charge near less electronegative atom
– Nonpolar molecules: affinity for electrons is the same and electrons are equally shared
8. Explain the properties of water that are important to life. 2.4 – Cohesion: hydrogen bonds hold water molecules together • EX. Leave pulls water upward from roots; seeds swell and germinate
– High specific heat: hydrogen bonds absorb heat when they break and release heat when they form, minimizing temp change • EX. Water stabilizes the temp of organisms and
– High heat of vaporization: many hydrogen bonds must be broken for water to evaporate
• EX. Evaporation of water cools body surfaces
– Lower density of ice: water molecules in an ice crystal are spaced relatively far apart because of H bonding
• EX. Because ice is less dense than water, lakes do not
freeze solid, allowing fish and other life in lakes to survive the winter
– Solubility: polar water molecules are attracted to ions and polar compounds, making these compounds soluble
• EX. Many kinds of molecules can move freely in cells
permitting a diverse array of chemical reactions
– Hydrophobic exclusion: water repels hydrophobic compounds, forcing them to associate together
• EX. Biological membranes have bilayer structure with
9. Describe the relationship between pH and hydrogen ion concentration, and explain how to interpret the pH scale. 2.5.1 – The higher the [H+], the lower the pH
– pH <7 is acidic, pH =7 is neutral, pH >7 is basic
10. Distinguish between an acid and a base. 2.5.1
– acid: any substance that dissociates in water to increase [H+] and lower pH
– base: any substance that combines with H+ when dissolved in water, lowering [H+] and increasing pH
11. Explain how buffers, such as the bicarbonate buffer system, stabilize the pH of solutions. 2.5.1
Buffers exist in solutions to maintain pH by releasing acid when too much base is present and, in a reciprocal manner, releasing base when too much acid is present.
Ch. 3/6 CARBS, NUCLEOTIDES, & ENZYMES 1. Recognize the general structures of monosaccharides, amino acids, and nucleotides, and describe the chemical properties of each. 3.2.1, 3.3.2, 3.4.1
monosaccharides: simplest sugar, C-H bonds with as few as 3 carbon atoms (plays central role in energy storage=6 carbons); linked by covalent bonds— structural isomers determine sweetness
amino acids: central carbon atom, amino group (-NH2), carboxyl group (- COOH), functional side group (R); linked by peptide bonds—chemical character is determined by R group
nucleotides: 5 carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base (purines-AG or pyrimidines-CT); linked by phosphodiester bonds—OH on sugar ring = RNA, H on sugar ring = DNA
2. Differentiate between glycosidic linkage, peptide bond, and phosphodiester bond.
glycosidic linkage: covalent bond between a sugar molecules and another group (may or may not be carbohydrate)
peptide bond: covalent bond between two amino acids
phosphodiester bond: covalent bond between nucleotides to form nucleic acids
3. Describe the functions of carbohydrates in cells. 3.2 -building blocks for carbon skeletons
-cell identity on outer surface
-energy storage (glucose, glycogen, starch—alpha linkage) -structure (cellulose, chitin—beta linkage)
4. How do the structures of starch, glycogen and cellulose affect their functions? 3.2
-starch and glycogen: alpha branching, allows for longer food reserve, easier to be broken due to branching rather than linkage
-cellulose: beta linkage, stronger than alpha branching à linkage is better for structures; resists tension, compression, and hydrolysis
5. Describe the functions of nucleotides in cells. 3.4.4 -nucleic acid building blocks (DNA, RNA)
-cellular energy carriers (ATP, GTP)
-electron acceptor/donor (NAD, NADP, FAD)
-carrier of chemical groups (ATP, CoA, UDP)
-regulatory (signaling) molecules (GTP, cAMP)
6. Explain how a catalyst increases the rate of a chemical reaction. 6.4.1
A catalyst lowers activation energy and makes the transition state more stable.
7. Describe the characteristics of enzymes. 6.4.2
-mostly proteins, some RNA
-lowers activation energy by stressing specific bonds
-different enzymes catalyze different, specific reactions
-can be reused
8. Explain how enzymes lower activation energies. 6.4.2 Enzymes stress specific chemical bonds in order to allow new bonds to form more easily.
9. Distinguish between substrate, active site, enzyme-substrate complex, and induced fit. 6.4.3
substrate: the ligand that binds to an enzyme
active site: the site where the substrate (ligand) binds to an enzyme
enzyme-substrate complex: the substrate fits into the enzyme and binds induced fit: the term that describes how the enzyme must alter its shape slightly for the substrate to fit and bind properly
10. Identify the different types of molecules that may act as enzymes. 6.4.4
-RNA: ribozymes may catalyze other molecules (intermolecular catalysis) or themselves (intramolecular catalysis)—rRNA play a key catalytic role in RNA production, with proteins providing the framework to correctly orient RNA subunits with respect to each other
11. Distinguish between enzyme cofactors and coenzymes. 6.4.4 -cofactor: additional chemical component, often metal ions found in active site, that assist enzyme function
-coenzyme: cofactor that is a nonprotein, organic molecule
12. Explain the effects of pH and temperature on enzyme activity. 6.4.5
-pH: when pH is not at optimal pH, the rate is not as fast as it has the potential to be. High pH = ionization, low pH = nonionization (affects ionization of R groups)
-temperature: increase in temp increases collisions, thereby speeding up rate, BUT when the temperature gets too high, the protein will change shape (denaturation/unfolding)—an increase in temperature can cause renaturation/refolding in some cases
13. Distinguish between competitive and noncompetitive enzyme inhibition. 6.4.5
competitive enzyme: will block substrate at active site
noncompetitive enzyme: will block substrate by entering enzyme at different site than where substrate binds
14. Explain allosteric regulation of enzymes. 6.4.5
Allosteric regulation can activate or inhibit enzymes—can bind to an area other an active site to stabilize an active form or inactive form (noncovalent/reversible)
15. Explain the control of protein function by phosphorylation. 9.1.3 Phosphorylation acts as a switch; if the protein is “off” before adding a phosphate, phosphorylation will turn it “on” and vice versa. The concentration of kinase will affect amount of phosphorylation (lots of kinase = lots of phosphorylation).
LEARNING OBJECTIVES FOR ENERGY AND METABOLISM (Ch. 6) 1. Define energy and distinguish between potential and kinetic energy. 6.1.1
-energy: capacity to do work
-potential energy: energy of motion (active energy)
-kinetic energy: stored energy (energy at rest)
2. State the First Law of Thermodynamics. 6.2.1
Energy cannot be created or destroyed; it can only change from one form to another (e.g. potential to kinetic).
3. State the Second Law of Thermodynamics and describe how it applies to biological systems. 6.2.2
Disorder in the universe (i.e. entropy) is continually increasing.
4. Define entropy, enthalpy and free energy. Explain how chemical reactions can be predicted based on changes in free energy. 6.2.3 -entropy (S): disorder in the universe
-enthalpy (H): total energy contained in a molecule’s chemical bonds -free energy: availability of energy to do work with temperature and pressure constant; a positive change in free energy means the reaction will not be spontaneous/not favorable while a negative change in free energy means the reaction will be spontaneous/favorable.
5. Distinguish between endergonic and exergonic reactions. Explain what is meant by a spontaneous reaction. 6.2.3
-endergonic: requires energy, not spontaneous, typically +ΔG/+ΔH/-ΔS -exergonic: doesn’t require energy to occur, spontaneous, typically -ΔG/- ΔH/+ΔS
-spontaneous reaction: additional energy is not required for the reaction to occur
*6. Recognize the general structures of nucleotides and describe their chemical properties. 3.4.1
-5 carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base (purines-AG or pyrimidines-CT); linked by phosphodiester bonds—OH on sugar ring = RNA, H on sugar ring = DNA
*7. Describe the functions of nucleotides in cells. 3.4.4 -nucleic acid building blocks (DNA, RNA)
-cellular energy carriers (ATP, GTP)
-electron acceptor/donor (NAD, NADP, FAD)
-carrier of chemical groups (ATP, CoA, UDP)
-regulatory (signaling) molecules (GTP, cAMP)
8. Describe the three main kinds of work carried out by cells. Fig 6.7 -chemical: biosynthesis, bioluminescence
-transport: voltage, concentration
9. Describe the structure of ATP and explain how ATP hydrolysis drives endergonic reactions. 6.3.1
-structure: 5-carbon sugar (ribose), 2 carbon-nitrogen rings (adenine), 3 phosphates
-ATP hydrolysis driving endergonic reactions: if cleavage of ATP ‘s terminal high-energy bond releases more energy than the other reaction consumes, the two reactions can be coupled, resulting in a net release of energy (-ΔG)--almost all endergonic reactions require less energy than released by ATP hydrolysis, so ATP is able to provide most energy a cell needs,
10. Describe energy coupling using ATP hydrolysis.
Energy coupling is the transfer of energy from an exergonic process to an endergonic process. Free energy from ATP hydrolysis is used to drive endergonic reactions.
Ch. 7 Cell Respiration
1. Distinguish between oxidation and reduction reactions. 6.1.2, 7.1.1 -LEO says GER (Lose Electrons Oxidation/Gain Electrons Reduction) -oxidation: process by which an atom or molecule loses an electron--Lose
Electrons Oxidation; atom or molecule that accepts an electron is an oxidizing agent
-reduction: process by which an atom or molecule gains an electron--Gains Electrons Reduction; atom or molecule that donates or gives away an electron is a reducing agent
2. Describe the structure of NAD, its role, and the role of B vitamins in energy metabolism. 7.1.2
Structure: 2 nucleotides (nicotinamide monophosphate-NMP +adenosine monophosphate-AMP) joined head to head; NMP is active part--readily reduced (accepts electrons)
NAD role: major electron carrier; when NAD is reduced by accepting 2 B vitamin role: B Vitamins act as coenzymes that are crucial in aiding enzymes in ATP and fatty acid production.
3. Explain the process of glycolysis, including reactants, products, and energy yield. 7.2.1
Process: anaerobic; glucose is converted into 2 pyruvates; each molecule of glucose yields 2 ATP in this process; consists of 10 rxns, first 5 in energy investment phase (priming, endergonic) and second 5 in energy payoff phase (splitting, exergonic)
Reactants: glucose, 2NAD+, 4 electrons, 2 ATP, 4 H+
Products: 2H+, pyruvate, 2H2O, 4 ATP (total yield of 2 ATP), 2NADH Energy yield: 2 ATP
4. Describe two ways in which ATP is generated in cellular respiration. 7.1.3 (p. 134-135)
a. Substrate-level phosphorylation: ATP is formed by transferring a phosphate group directly to ADP from a phosphate-bearing intermediate or substrate; in glycolysis, the chemical bonds of glucose are shifted around in
reactions that provide the energy required to form ATP by substrate-level phosphorylation
b. Oxidative phosphorylation: ATP is synthesized by ATP synthase (which is both an enzyme and a channel) using energy from a proton gradient that is formed by high-energy electrons harvested by the oxidation of glucose and passing down an electron transport chain (how ATP is produced most by eukaryotes and aerobic prokaryotes)
5. Name and describe the four stages of cellular respiration, identifying specifically where in the cell (prokaryotic and eukaryotic) each occurs. Figure 7.5; 7.2. 7.3, 7.4
a. GLYCOLYSIS: cytoplasm in euk and prok
b. PYRUVATE OXIDATION: mitochondria in euk, in cytoplasm and at plasma membrane in prok
c. KREBS CYCLE/CITRIC ACID CYCLE/TCA: mitochondrial matrix/inner membrane of mitochondria in euk, cytosol in prok
d. OXIDATIVE PHOSPHORYLATION: mitochondrial cristae in euk, cell membrane in prok
6. Describe two different metabolic pathways that pyruvate can enter. 7.2.2, 7.3.1, 7.7.2
a. Oxidation of pyruvates--cleaves off one of pyruvate’s 3 carbons which becomes CO2, remaining 2-carbon compound (acetyl) attaches to coenzyme A to produce acetyl-CoA. In this rxn, 2 electrons and 1 proton are transferred to NAD+ to reduce it to NADH with a 2nd proton donated. b. Fermentation--uses reduction of all or part of pyruvates to oxidize NADH back to NAD+, executed copiously by bacteria
7. Identify the reactants and products of pyruvate oxidation. 7.3.1 (p. 139)
-Reactants: pyruvates, NAD+, CoA
-Products: acetyl-CoA, NADH, CO2, H+
8. Identify the reactants and products of the Krebs cycle and describe its role. 7.3.2 (p.139-140)
-Reactants: acetyl-CoA, 3NAD+, FAD, ADP + P, OAA
-Products: 1 ATP, 3 NADH, 1 FADH2, CO2, CoA-SH, OAA
9. Describe how the movement of electrons along the electron transport chain generates a proton gradient. 7.4.1 (p.143) -The first protein to receive the electrons is the membrane-embedded enzyme NADH dehydrogenase.
-A carrier called ubiquinone then passes the electrons to a protein-cytochrome complex called the bc1 complex.
-The electrons are then carried by cytochrome C to the cytochrome oxidase complex. This complex uses 4 electrons to reduce a molecule of oxygen; each oxygen then combines with 2 protons to form water. -Protons are produced when electrons are transferred to NAD+.
-As the electrons are passed along the ETC, the energy they release transports protons out of the matrix and into the intermembrane space (concentration gradient).
***The flow of highly energetic electrons induces a change in the shape of pump proteins, causing them to transport protons across the membrane. The increasing electronegativity with each pump propels the protons down the ETC.
10. Explain chemiosmosis, including a description of how ATP synthase works. 7.4.2 (p.144)
-Chemiosmosis: ATP is driven by a diffusion force similar to osmosis. Because the mitochondrial matrix is negative compared with the intermembrane space, protons are attracted to the matrix. The higher outer concentration of protons
drives protons back in by diffusion, but because membranes are relatively impermeable to ions, this occurs slowly.
-ATP synthase: enzyme channel that uses the energy of the gradient to catalyze the synthesis of ATP; the new ATP is transported by facilitated diffusion to the many places in the cell where enzymes require energy to drive endergonic reactions
11. Explain the maximum yield of ATP from a molecule of glucose and the efficiency of this energy conversion. 7.5
The maximum yield is approx. 30-32 ATP. oxidizing glucose to pyruvates via glycolysis yields 2 ATP directly, and 2 × 2.5 = 5 ATP from NADH, oxidation of pyruvates to acetyl-CoA yields another 2 × 2.5 = 5 ATP from NADH, the Krebs cycle produces 2 ATP directly, 6 × 2.5 = 15 ATP from NADH, and 2 × 1.5 = 3 ATP from FADH2; NADH produced in the cytoplasm by glycolysis needs to be transported into the mitochondria by active transport, which costs one ATP per NADH transported (causing 30 vs 32 ATP)
12. Explain why the maximum yield of ATP is rarely obtained. 7.8, Figs. 23.7, 31.1 (symport)
The max yield is limited by the fractional number of ATP produced by NAHD and FADH2, which NADH shuttle transported to the mitochondria, the other uses the proton motor force is used for (moving ADP to matrix, proton symport), and intermediates in anabolism.
13. Explain feedback regulation and describe two keys points at which it is used to regulate cellular respiration. 6.5.2, 7.6.1 (The 3rd paragraph in 6.5.2, beginning with ”In the hypothetical pathway…”, refers to something that is not in our text.)
-Feedback regulation: control mechanism whereby an increase in the concentration of some molecules inhibits the synthesis of that molecule. a. in glycolysis: control point at phosphofructokinase (which catalyzes the conversion of fructose phosphate to fructose bisphosphate); first reaction of glycolysis that is not readily reversible; ATP itself and citrate (Krebs cycle intermediate) are allosteric inhibitors--high levels of both ATP and citrate inhibit phosphofructokinase. When ATP is in excess or when the Krebs cycle is producing citrate faster than it is being consumed, glycolysis is slowed. b. in pyruvate oxidation: control point at pyruvate dehydrogenase (which converts pyruvate to acetyl-CoA); inhibited by high levels of NADH; another control point in the Krebs cycle is citrate synthetase (which catalyzes the first reaction, the conversion of oxaloacetate and acetyl-CoA into citrate)-- high levels of ATP inhibit citrate synthetase (as well as phosphofructokinase, pyruvate dehydrogenase, and two other Krebs cycle enzymes), slowing down the entire catabolic pathway.
14. Describe two ways that prokaryotes can produce ATP entirely anaerobically. 7.7
-anaerobic respiration: many prokaryotes use sulfur, nitrate, carbon dioxide, or even inorganic metals as the final electron acceptor in place of oxygen-- amount of free energy released is lower than with oxygen because of lower electronegativity; ATP production is less
-fermentation: the electrons generated by glycolysis are donated to organic molecules
15. Describe fermentation, explain its role, and distinguish between ethanol and lactic acid fermentation. 7.7.2
-Fermentation: anaerobic process that occurs after pyruvate has been produced through glycolysis; allows cells to regenerate NAD+ for glycolysis -Ethanol fermentation: occurs in yeast, the molecule that accepts electrons from NADH is derived from pyruvates, the end-product of glycolysis, Yeast enzymes remove a terminal CO2 group from pyruvate through decarboxylation, producing a 2-carbon molecule called acetaldehyde. The CO2 released causes bread made with yeast to rise. The acetaldehyde accepts a pair of electrons from NADH, producing NAD+ and ethanol, source of the ethanol in wine and beer
-Lactic acid fermentation: regeneration of NAD+ in the absence of oxygen without decarboxylation; for example, muscles use the enzyme lactate dehydrogenase to transfer electrons from NADH back to the pyruvates that is produced by glycolysis. This reaction converts pyruvates into lactic acid and regenerates NAD+ from NADH, allowing glycolysis to continue as long as glucose is available
16. Briefly describe how proteins and fats can be used to make ATP in cellular respiration. 7.8
-Proteins: first broken down into their individual amino acid (deamination), and a series of reactions converts the carbon chain that remains into a molecule that enters glycolysis or the Krebs cycle. The reactions of cellular respiration then extract the high-energy electrons from these molecules and put them to work making ATP
-Fats: broken down into fatty acids plus glycerol, oxidized in the matrix of the mitochondrion. Enzymes progressively remove 2-carbon acetyl groups from the terminus of each fatty acid, nibbling away at the end until the
entire fatty acid is converted into acetyl groups. Each acetyl group is combined with coenzyme A to form acetyl-CoA (known as beta oxidation)
Chapter 8 Photosynthesis
1. Describe the four ways that organisms obtain carbon and energy. 23.4.1
a. Photoautotroph: energy source = light; carbon source = CO2, HCO3-, or related compound (cynobacteria, bacteriachlorophyll)
b. Chemolithoautotrophs: energy source = inorganic substances (prokaryotes on the ocean floor)
c. Photoheterotrophs: energy source = light; carbon cource = organic molecules (nonsulfur bacteria)
d. Chemoheterotrophs: energy = organic molecules; carbon source = organic molecules (decomposers, most pathogens, humans, nonphotosynthetic eukaryotes)
2. Write the balanced equation for photosynthesis and identify which molecules are oxidized or reduced. 8.1.1
6CO2 + 12H2O + sunlight → C6H12O6 (glucose) + 6H2O + 6O2 In photosynthesis, CO2 is reduced to glucose using electrons gained from the oxidation of water. The oxidation of H2O and the reduction of CO2 requires energy that is provided by light.
3. Compare the structure of a chloroplast with that of a mitochondrion. 8.1.2
A mitochondrion's complex structure of internal and external membranes contribute to its function. The same is true for the structure of the chloroplast. The internal membrane of chloroplasts, called the thylakoid membrane, is a continuous phospholipid bilayer organized into flattened sacs
that are found stacked on one another in columns called grana (singular, granum). The thylakoid membrane contains chlorophyll and other photosynthetic pigments for capturing light energy along with the machinery to make ATP. Connections between grana are termed stroma lamella. Surrounding the thylakoid membrane system is a semiliquid substance called stroma. The stroma houses the enzymes needed to assemble organic molecules from CO2 using energy from ATP coupled with reduction via NADPH. In the thylakoid membrane, photosynthetic pigments are clustered together to form photosystems, which act as large antennas, gathering the light energy harvested by many individual pigment molecules.
4. Describe the endosymbiotic origin of chloroplasts. 24.1.3 All chloroplasts are likely derived from a single line of cyanobacteria, but the organisms that host these chloroplasts are not monophyletic. This apparent paradox is resolved by considering the possibility of secondary, and even tertiary endosymbiosis. Red and green algae both obtained their chloroplasts by engulfing photosynthetic cyanobacteria. The brown algae most likely obtained their chloroplasts by engulfing one or more red algae, a process called secondary endosymbiosis.
5. Identify specifically the location of the light reactions and carbon fixation in the chloroplast.
-light reactions: photosystems (photosynthetic pigments clustered together in thylakoid membrane)
-carbon fixation: stroma
6. Identify the reactants and products of the Calvin cycle 8.6.2 -reactants: 6CO2, 18ATP, 12NADPH, H20
-products: 2 G3P, 16 Pi, 18 ADP, 12 NADP+
7. Describe the three major phases of the Calvin cycle and the role of Rubisco. 8.6.1, 8.6.2
a. Carbon fixation: generates 2 molecules of PGA
-3 RuBP + 3 CO2 → 6 PGA
2. Reduction: PGA is reduced to G3P by reverse-glycolysis rxns -6 PGA + 6 ATP + 6 NADPH → 6 G3P
c. Regeneration: PGA is used to regenerate RuBP
-5 G3P + 3 ATP → 3 RuBP
**G3P is product; 3 turns of cycle are needed to produce one molecule of G3P; 6 turns needed to synthesize one glucose molecule
-Rubsico: enzyme that carries out carbon fixation; catalyzes primary chemical reaction by which inorganic enters the biosphere; 16-subunit enzyme found in stroma; most abundant protein on earth, though slow
8. Describe the nature of electromagnetic radiation and visible light. 8.3.1
Light is a form of electromagnetic energy. The wave nature of light produces an electromagnetic spectrum based on wavelength and frequency. The shorter the wavelength, the greater the energy. Visible light occupies a very small part of the spectrum, approx. 400 nm to 740 nm (VIBGYOR--violet, indigo, blue, green, yellow, orange, red--with violet at 400 nm and red at 740 nm).
9. Identify which wavelengths/colors of visible light are most effective in photosynthesis. 8.3.2
Chlorophyll a and chlorophyll b absorb violet-blue and red light best. Neither absorb photons with wavelengths between approx. 500-600 nm; rather, light of these wavelengths get reflected. Chlorophyll b’s absorption
spectrum is shifted toward the green wavelengths. Because chlorophyll b can absorb green-wavelength photons that chlorophyll a cannot, this greatly increases the proportion of photons in sunlight that plants can harvest. The action spectrum (relative effectiveness of different wavelengths of light in promoting photosynthesis corresponds to the absorption spectrum of chlorophylls.
10. Identify the major pigments involved in plant photosynthesis and the roles of each. 8.3.2, 8.3.3
-chlorophylls (principal photosynthetic pigments): absorb photons within narrow energy ranges (violet-blue and red) at high efficiency -carotenoids (accessory pigments): absorb photons with a wide range of energies but with less efficiency, capture energy from light composed of wavelengths not efficiently absorbed by chlorophylls; also can act as general-purpose antioxidants to lessen damage of free radicals (aka certain redox rxns that occur in the chloroplast)
11. Differentiate between photosystem, antenna complex, reaction center. 8.4.2
-photosystem: an organized complex of chlorophyll, other pigments, and proteins that traps light energy as excited electrons
-antenna complex: complex of hundreds of pigment molecules in a photosystem that collects photons and feeds the light energy to a reaction center, light-harvesting complex captures photons from sunlight and channels them to the reaction center chlorophylls. In chloroplasts, light harvesting complexes consist of a web of chlorophyll molecules linked together and held tightly in the thylakoid membrane by a matrix of proteins. Varying amounts of carotenoid accessory pigments may also be present. The
protein matrix holds individual pigment molecules in orientations that are optimal for energy transfer.
- The excitation energy resulting from the absorption of a photon passes from one pigment molecule to an adjacent molecule on its way to the reaction center . After the transfer, the excited electron in each molecule returns to the low-energy level it had before the photon was absorbed. Consequently, it is energy, not the excited electrons themselves, that passes from one pigment molecule to the next. The antenna complex funnels the energy of many excited electrons to the reaction center.
-reaction center: transmembrane protein complex in a photosystem that receives energy from the antenna complex, exciting an electron that is passed to an acceptor molecule.
• reaction center of purple photosynthetic bacteria is simpler than the one in chloroplasts--a pair of bacteriochlorophyll a molecules acts as a trap for photon energy, passing an excited electron to an acceptor precisely positioned as its neighbor. In this reaction center, what is transferred is the excited electron itself, and not just the energy, as was the case in the pigment–pigment transfers of the antenna complex. This difference allows the energy absorbed from photons to move away from the chlorophylls, and is the key conversion of light into chemical energy.
12. Explain the functions of photosystem I and of photosystem II. Explain why two photosystems are required to reduce NADP. 8.5.2, 8.5.3 (p. 166-169)
-Photosystem I: absorption peak = 700 nm; reaction center pigment = P700; transfers electrons ultimately to NADP+, producing NADPH; absorbs
photons, exciting electrons used to reduce NADP+ to NADPH; electrons replaced by electron transport from photosystem II
-Photosystem II: absorption peak = 680 nm; reaction center pigment = P680; generates oxidation potential high enough to oxidize water to replace its electrons transferred to photosystem I; absorbs photons, exciting electrons that are passed to plastoquinone (PQ)
-Cyclic photophosphorylation limits electron sources. This noncyclic transfer of electrons allows the oxidation of water to serve as an alternative source of electrons. An overall flow of electrons from water to NADPH is created.
13. Explain how photosynthesis generates O2. 8.2.3 (p. 160) van Niel’s generalized equation for photosynthesis: CO2 + 2H2A + light energy → (CH2O) + H20 + 2 A
In this equation, H2A = an electron donor (which is water in photosynthesis). The product “2 a” comes from splitting the H2A. In real life, O2 is the product of the splitting of H2O.
14. Describe how a proton gradient drives ATP synthesis in the chloroplast. 8.5.4 (p. 168)
The chloroplast has ATP synthase enzymes in the thylakoid membrane that form a channel, allowing protons to go back to the stroma. As protons pass out of the thylakoid through the ATP synthase channel, ADP is phosphorylated to ATP and released into the stroma.
15. Compare chemiosmosis in chloroplasts and mitochondria. 7.4.2, 8.5.4 (p. 168)
Both use a proton gradient by electron transport that generates ATP by chemiosmosis. In mitochondria, the protons reenter the matrix through ATP synthase, and in chloroplasts, protons reenter the stroma.
16. Compare the roles of CO2 and H2O in respiration and photosynthesis.
In cellular respiration, a glucose molecule combines with oxygen to form ATP with CO2 and H2O as waste products Oxygen is absorbed and carbon dioxide is released. In photosynthesis, the reciprocal of this occurs. Carbon dioxide and water are combined as reactants, yielding glucose and oxygen as products. Carbon dioxide is absorbed and oxygen is released.
Describe the events of binary fission, prokaryotic cell division. 10.1.1, 10.1.2
1. Prior to cell division, bacterial DNA molecule replicates. The replication begins at a specific site (origin of replication).
2. Replication enzymes move out in both directions from origin and make copies of each strand in the DNA duplex and continue until they meet at another specific site (terminus of replication).
3. As the DNA is replicated, the cell elongates, and the DNA is partitioned in the cell such that the origins are at the ¼ and ¾ positions in the cell and the termini are oriented toward the
middle of the cell.
4. Septation begins, in which new membrane and cell wall material begin to grow and form a septum at approximately the midpoint of the cell.
5. When the septum is complete, the cell pinches in two, and two daughter cells are formed, each containing a bacterial DNA
Describe the structure of a eukaryotic chromosome. 10.2.2
– Contains single DNA molecule that runs uninterrupted through chromosome’s entire length
– DNA duplex is tightly bound to and wound around histone proteins (positively charged because of abundance of amino acids) o This complex is called the nucleosome.
– Final organization of chromosome involves radial looping into rosettes around a protein
Differentiate between chromosome, chromatin and chromatid. 10.2.2
– Chromosome: packaged structure containing DNA
– Chromatin: complex of DNA and protein
– Chromatid: replica of a single chromosome (sister chromatids held together at centromeres by cohesin proteins)
Describe the events of the 5 stages of the eukaryotic cell cycle. 10.3.1, 10.4.1
1. G1 (gap phase 1): primary growth pahse of the cell, refers to filling the gap between cytokenesis and DNA synthesis (longest phase) 2. S (synthesis): phase in which the cell synthesizes a replica of its DNA genome
3. G2 (gap phase 2): second growth phase, involves preparation for separation of newly replicated genome, fills gap between DNA synthesis and beginning of mitosis; microtubules begin to reorganize to form spindle
*****G1 + S + G2 = INTERPHASE*****
4. Mitosis: phase of cell cycle in which spindle apparatus assembles, binds to chromosomes, and moves sister chromatids apart; essential
step in separation of 2 daughter genomes; traditionally subdivided into prophase, prometaphase, metaphase, anaphase, and telophase 5. Cytokenesis: phase of cell cycle when cytoplasm divides, creating 2 daughter cells; in animal cells the microtubule spindle helps position a contracting ring of actin that constricts like a drawstring to pinch the cell in 2; in cells with a cell wall, such as plant and fungal cells, a plate forms between the dividing cells
Describe the events that take place during each stage of the five stages of mitosis, including the changes in the structure and position of the chromosomes at each step. 10.5.1-10.5.5
– Prophase: chromosomes condense and become visible, chromosomes appear as 2 sister chromatids held together at centromere, cytoskeleton is disassemblesd, spindle begins to form, Golgi and ER are dispersed, nuclear envelope breaks down
– Prometaphase: chromosomes attach to microtubules at kinetochores, each chromosome is oriented such that the kinetochores of sister chromatids are attached to microtubules from opp. poles,
chromosomes move to equator of cell
– Metaphase: all chromosomes are aligned at equator of cell aka metaphase plate; chromosomes attached to opposite poles and are under tension
– Anaphase: proteins holding centromeres of sister chromatids are degraded, freeing individual chromosomes, chromosomes are pulled to opposite poles (anaphase A), spindle poles move apart (anaphase B)
– Telophase: chromosomes are clustered at opposite poles and decondense, nuclear envelopes re-form around chromosomes, Golgi complex and ER re-form
Compare cytokinesis in plant and animal cells. 10.5.6 – Animal cells: a belt of actin pinches off the daughter cells, creating a cleavage furrow around cell’s circumference
– Plant cells: a cell plate partitions the membrane and grows outward until it reaches the interior surface of the plasma membrane and fuses with it, dividing the cell in 2; cellulose is laid on the new membranes, creating 2 new cell walls
Explain the importance of checkpoints during the eukaryotic cell cycle. 10.6.2
– Checkpoint: marker where the cycle can be delayed or halted; used to assess internal state and to integrate external signals
Ch. 11 Sexual Reproduction and Meiosis Differentiate between haploid and diploid numbers of chromosomes in a species. 10.2.1
– Haploid: cell with half the normal number of chromosomes – Diploid: fusion of haploids
Compare the number of chromosomes in gametes and zygotes 11.1.1
– Gametes: contain 2 chromosomes
– Zygotes: contain 2 copies of each chromosome
Describe the sexual life cycle in animals. Distinguish between somatic and germ-line cells. 11.1.2
– Sexual life cycle: zygote undergoes mitosis to produce diploid cells, then later in the cycle, some of the diploid cells undergo meiosis to produce haploid gametes
– Somatic-line cells: form all cells in adult body, will eventually undergo meiosis
– Germ-line cells: cells produced gametes set aside from somatic cells early in development, by meiosis
4. Distinguish between homologous chromosomes, sister chromatids, and non-sister chromatids. 10.2.2, Fig. 10.6 – Homologous chromosomes: maternal and paternal copies of same chromosome
– Sister chromatids: two replicas of a single chromosome held together at centromeres by cohesin proteins after DNA replication
– Non-sister chromatids: chromatids of 2 homologous chromosomes
5. Describe the process and consequences of homologous pairing, including crossing over. 11.2.1-11.3.1
• Process: prophase I of meiosis, homologous chromosomes find each other and become closely associated then crossing over occurs at chiasmata (genetic recombination)
8. Identify what 3 events, unique to meiosis, occur during meiosis I. 11.3.1 – 11.3.2
P1: homologues pair and cross over
M1: paired homologues align
A1: Sister chromatids remain connected at centromere and segregate together
9. Differentiate between how chromosomes or chromatids separate during anaphase of mitosis, anaphase I of meiosis and anaphase II of meiosis. 10.5.4, 11.3.3, 11.3.5
Mitosis: chromosomes are pulled to opposite poles
Anaphase I: sister chromatids remain connected at the centromere and segregate together
Anaphase II: sister chromatids are pulled to opposite poles of the cells
13. Compare mitosis and meiosis II. 11.3.5
• Mitosis and meiosis II are essentially the same processes.
14. Identify the four distinct features of meiosis and describe their molecular mechanisms 11.4.1
1. Homologous pairing and crossing over joins maternal and paternal homologues during meiosis I.
2. Sister chromatids remain connected at the centromere and segregate together during anaphase of meiosis I.
3. Kinetochores of sister chromatids are attached to the same pole in meiosis I and to opposite poles in mitosis.
4. DNA replication is suppressed between the two meiotic divisions.
Ch. 12 Patterns of Inheritance
Explain how Mendel’s particulate theory of inheritance differed from the blending theory of inheritance. 12.2
• The blending theory of inheritance predicted a hybrid offspring of an intermediate color. Mendel’s theory proposed different plants inherited each trait intact, as a discrete characteristic.
3. Distinguish between: gene/allele/loci; dominant /recessive; homozygous/heterozygous; genotype/phenotype. 12.2.2 Gene: a
Allele: one of two or more alternative states of a gene
Loci: location of a gene in a chromosome
Dominant: expressed when present in heterozygous or homozygous condition
Recessive: expressed when present in only homozygous condition; “hidden” in heterozygous condition
Homozygous: two identical alleles of the same gene
Heterozygous: two different alleles of the same gene
Genotype: genetics of a single trait or set of traits
Phenotype: physical appearance or functional expression of a single trait or set of traits
4. Explain the relationship of an allele to a gene. 12.2.2 • Not all genes are identical, so to distinguish different states of genes, we call them alleles.
5. Use a Punnett square to predict the results of a monohybrid cross, stating the phenotypic and genotypic ratios of the F2 generation. 12.2.3
Phenotypic - 3 purple:1 white
Genotypic - 1 PP:2Pp:1pp
6. Use a Punnett square to predict the results of a dihybrid cross and state the phenotypic and genotypic ratios of the F2 generation. 12.3.1
Phenotypic - 3 purple:1 white
7. State Mendel’s law of independent assortment and describe how this law can be explained by the behavior of chromosomes during meiosis. 12.3.1
Law of independent assortment:
8. Explain how genotype determines phenotype. 12.5 The frequency of dominant/recessive alleles determines the outward appearance.
9. Explain polygenic inheritance and quantitative traits. Give some examples. 12.6.1
10. Explain the genetic basis of pleotropic effects on inheritance. Give some examples. 12.6.2.
Pleotropic: when one gene affects multiple traits (Ex. Sickle cell anemia)
11. Explain how the phenotypic expression of a heterozygote is affected by complete dominance, incomplete dominance, and codominance. 12.6.4
Complete dominance: the presence of one dominant allele dominates the entire genotype
Incomplete dominance: the phenotypic result is an intermediate of the two alleles (red + white = pink)
Codominance: the phenotypic result includes the presence of both alleles (blood type)
12. Explain how phenotypes can be affected by the environment. Give some examples. 12.6.5
Environmental effects: outside environments can affect the expression of genotype, and some alleles are internally affected (soil in Mendel’s yard for pea plants, heat-sensitive alleles in Siamese cats)
Chapter 13: Chromosomal Basis of Inheritance Understand and describe how chromosomes are the vehicles of Mendelian inheritance, and explain the chromosomal basis of sex linkage. 13.1.1
Genes located on chromosomes determine Mendelian traits. A trait determined by a gene on the X chromose is referred to as sex-linked because there is a correlation between trait expression and the sex of the individual. For example, a recessive sex-linked trait is always expressed in males but expressed in females only if they are homozygous.
Describe sex determination in a variety of organisms. 13.1.2 Humans: Y chromosome determines maleness
Drosophila: dosage compensation achieved by increasing level of expression on the male chromosome
Explain why recombination frequency is related to genetic distance. 13.2.1
• The further apart genes are, the more likely crossing over will occur, thus the higher the recombination frequency
Explain how changes in chromosome number can have drastic effects. 13.4.1
An additional or lower chromosome number often causes the organism to die before even being born.
Identify some important genetic disorders. 13.5.2
• Hemophilia: sex-linked recessive, blood fails to clot
• Sickle-cell: autosomal recessive, blood circulation is poor • Huntington: autosomal dominant, brain tissue gradually deteriorates in the middle age
Ch. 14 DNA
Describe the contributions of Griffith, Avery, and Hershey and Chase to identifying DNA as the hereditary molecule. 14.1
• Griffith: mice and virus experiment deduced that genetic material was transferred between the cells
• Avery: reperformed Griffith’s experiment but removed nearly all of the protein and found that the substance in the transformation had the same chemistry as DNA, same physical and chemical behavior as DNA, was not affected by protein and lipid extraction was not destroyed by protein or RNA-digesting enzymes, and was destroyed by DNA digesting enzymes, concluding that DNA was the hereditary material
• Hershey-Chase: 32P and 35S DNA vs protein experiment uncovered that DNA, not protein, held the genetic information that viruses inject into bacteria
Identify the nucleotide components in DNA and the bonds that hold them together. 14.2.1
• Components: 5-C sugar, phosphate group, nitrogenous base (purine or pyrimidine)
• Phosphodiester bond linkage (phosphates linked to two sugars by a pair of ester bonds)
Describe the evidence that Watson and Crick used to deduce the structure of DNA. 14.2.2, 14.2.3
Watson and Crick used Chargraff’s rules (A/T and C/G pairing) and Rosalind Franklin’s experimental results with X-Ray diffraction to create their structure.
Describe Watson and Crick’s structure for the DNA molecule, including complementary base pairing and the antiparallel nature of the phosphodiester backbone. 14.2.4
The molecule had 2 strands of long polymers of nucleotides of repeating sugar and phosphate units that ran antiparallel of each other with specific, complementary base pairs (A forms 2 H bonds with T and C forms 3 H bonds with G).
Describe semiconservative DNA replication. 14.3
One strand of the parental duplex remains in tact in the daughter strands with a new complementary strand built for each parental strand consisting of new nucleotides. Daughter strands would consist of one parental strand and one newly synthesized strand.
Describe origins of replication, bidirectional synthesis, and replication forks. 14.4
• Origins of replication: specific site where replication begins • Bidirectional synthesis: synthesis occurs in opposite directions on the chromosome from an origin until a termination site
• Replication forks: where DNA strands separate for replication to begin
Identify what is required to synthesize DNA, including the functions of helicase, single-strand binding protein, gyrase,primase, DNA polymerases I and III, and DNA ligase. 14.4, Table 14.1 • Helicase: unwinds double helix
• SSB: stabilizes single-stranded regions
• Gyrase: relieves torque (tension)
• Primase: synthesizes RNA primers
• DNA Pol I: erases primer and fills gaps
• DNA Pol III: synthesizes DNA
• DNA ligase: joins ends of DNA segments; DNA repair
Explain why DNA synthesis is not continuous on both strands. Compare DNA replication on the leading and lagging strands. Describe Okazaki fragments. 14.4.2
DNA synthesis is semidiscontinuous because of its antiparallel nature. One strand must have primers added as the helix opens. On the leading strand, DNA replication is continuous using DNA Pol III while the lagging strand has discontinuous replication using DNA Pol I for removal and replacement of primer segments and DNA Pol II for synthesis of Okazaki fragments. Okazaki fragments fill in the gaps of the lagging strand.
Describe the DNA replication complex (replisome). 14.4.3
The replisome has 2 main subcomponents: the primosome and the complex of two DNA Pol III enzymes, one for each strand. The primosome has primase and helicase with accessory proteins. The two Pol III complexes include two synthetic core subunits, each with its own beta subunit. The entire replisome complex is held together by a number of proteins that include the clamp loader.
Describe how the problem of Eukaryotic chromosomal end replication is handled. 14.5
Eukaryotic replication uses multiple origins, uses both DNA polymerase and DNA polymerase, and has telomeres at its ends.
Explain why DNA repair systems are needed. Give some examples of mutagens. Describe excision repair of DNA. 14.6.1
Errors in DNA replication and exposure to agent that can damage DNA lead to mutations. Mutagens are agents that increase the number of mutations above background levels, such as sunlight in the ozone and chemical mutagens in diets and environments. Excision repair is the most common form of repair. A damaged region is recognized, removed, and the information on the undamaged strand is used as a template to resynthesize.
Ch. 15 Genes
Explain why “one gene-one enzyme” was later modified to “one gene-one polypeptide”. Describe some exceptions to this relationship in eukaryotes. 15.1.1
• Many enzymes contain multiple polypeptide subunits, each encoded by a separate gene. However, eukaryotic genes are more complex than prokaryotic, and some enzymes are composed of RNA, an intermediate in the production of proteins.
Explain how the central dogma of molecular biology relates to information flow in cells. 15.1.2
• The central dogma shows the order of information flow, from the gene (DNA) to an RNA copy of the gen, and the RNA copy directed to the sequential assembly of a chain of amino acids into a protein.
Describe the major types of RNA in cells and give their roles. 15.1.2 • mRNA: RNA transcript used to direct the synthesis of polypeptides, carry the DNA message
• rRNA: found in ribosomal subunits, critical to its function • tRNA: interacts with mRNA and amino acids to interpret info in mRNA and help position the amino acids on the ribosome
• snRNAs: part of the machinery involved in nuclear processing of eukaryotic pre-mRNA with splicing
• SRP RNA: mediates where some proteins are synthesized by ribosomes on RER
• Small RNAs: involved in gene expression
Describe the three stages of transcription. 15.3.1, 15.4.2 1. Initiation – requires 2 sites (promoter—found upstream, forms a recognition/binding site for RNA polymerase—and start site) as well as a signal to end transcription (terminator), 1st step is binding of RNA polymerase to the promoter, then the
polymerase unwinds the DNA helix
2. Elongation – involves decoding, peptide formation, and
translocation; 2nd charged tRNA can bind to empty A site,
requires elongation factor to bind to tRNA, peptide bond can then form, addition of successive amino acids occurs as a cycle
3. Termination – elongation continues until the ribosome
encounters a stop codon, stop codons are then recognized by release factors which release the polypeptide from the ribosome
Compare DNA polymerase with RNA polymerase. 15.3.1 DNA polymerase needs a primer to initiate synthesis, is double stranded, uses thymine as a base, and has a single H branch. RNA polymerase doesn’t need a primer to initiate synthesis, is single stranded, uses uracil as a base, and has a single OH branch.
Describe how eukaryotic primary RNA transcripts are modified post transcriptionally. 15.4.3
The first base in the transcript is usually A or G, and this is modified by the addition of GTP to the 5’ PO4 group, creating the 5’ cap. A series of A residues, called the 3’ poly-A tail, is added, after the eukaryotic transcript is cleaved downstream, by the enzyme poly-A polymerase.
Differentiate between introns and exons. 15.5
• Introns are not always present and serve as place holders between exon, later removed, while exons are always present and can exist without introns.
Describe how the spliceosome processes a primary transcript. 15.5.1 • The spliceosome recognizes intron-exon junctions and begins with the cleavage of the 5’ end of the intron. This 5’ end becomes attached to the 2’ OH of the branch point A, forming a branched structure. The 3’ end of the first exon is then used to displace the 3’ end of the intron, joining the two exons together and releasing the intron.
Explain how complex eukaryotes, such as humans, can produce many more proteins than they have genes. 15.5.2
• Genes can code for multiple proteins.
Describe the structure and function of tRNA. 15.6.1
tRNA can be folded into a 2-D cloverleaf type of structure which is then folded in space to form an L-shaped 3-D molecule that has an amino acid acceptor stem at the 3’ end and an anticodon loop at the bottom of the clover leaf.
Describe the structure of a ribosome and describe the functions of the different tRNA binding sites on the ribosome. 15.6.3 A ribosome is composed of a large subunit and a small subunit. It has 3 binding sites: P (binds to the tRNA attached to the growing peptide chain), A (binds to the tRNA carrying the next amino acid to be added), and E (binds the tRNA that carried the previous amino acid added).
Describe two functions of the ribosome, including the role of peptidyl transferase. 15.6.3
Ribosomes decode the transcribed message and form peptide bonds. Peptidyl transferase, located in the large subunit, is required to form peptide bonds.
Describe the three stages of translation, including their energy sources. 15.7.2
1. Initiation (uses
2. Elongation - matching the tRNA anticodon with mRNA codon, peptide bond formation, translocation of the ribosome (uses GTP)
Compare gene expression in prokaryotes and eukaryotes. 15.4, 15.7.1, Table 15.2
Contrast the different kinds of point mutations, including base substitutions, silent, missense, nonsense, and frame shift mutations. 15.8.1
• Base substitutions – substitution of one base pair for another • Silent mutation – amino acid is not altered by base substitution • Missense – amino acid is altered by base substitution
• Nonsense – transcribed codon is converted to a stop codon • Frame shift – reading frame is shifted by insertion of a addition or deletion of a single base
Ch. 16 Control of gene expression
Compare the control of enzyme production by induction and repression. 16.3.1
• Induction occurs when enzymes for a certain pathway are produced in response to a substrate.
o EX. A bacterium encounters lactose and begins to make the enzymes necessary to utilize lactose but will not do so if no lactose is present.
• Repression occurs when bacteria capable of making biosynthetic enzymes do not produce them.
o EX. Tryptophan is available, so bacterium do not synthesize the enzymes necessary to make tryptophan but will in its absence.
Describe the roles of the following factors in eukaryotic gene regulation: promoter, enhancer, general transcription factors (GTFs), and specific TFs. 16.4.2
– Promoter: form the binding sites for general transcription factors – Enhancer: binding site of specific transcription factors
– General transcription factors (GTFs): necessary to establish productive initiation and required for transcription to occur (but do not increase rate above basal rate)
– Specific TFs: act in a tissue- or time-dependent manner to stimulate higher levels of transcription than the basal level
Describe the roles of coactivators and mediators. 16.4.3 – Coactivators and mediators act by binding the transcription factor and then binding to another part of the transcription apparatus. Mediators are essential to the function of some transcription factors, but not all transcription factors require them. The number of coactivators is much smaller than the number of transcription factors because the same coactivator can be used with multiple transcription factors.
Describe methylation and its role in gene regulation. 16.5.1 – Methylation blocks the accidental transcription of “turned-off” genes. This ensures that once a gene is off, it stays off.
Describe RNA interference 16.6
– RNA interference involves the production of siRNAs which act post transcriptionally to control gene expression.
Describe RNA editing. 16.6.4
– The editing of mature mRNA transcripts can produce an altered mRNA that is not truly encoded in the genome.