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Katie Jurek’s BSC2010 Final Exam Review This is not a comprehensive list, but simply a guide of what I’ve seen most often in the past. Ch. 1 – Introduction Cell Theory 1. Cells are made from other cells. 2. Cells make up all living things. Q: What is DKPCOFGS? - Domain kingdom phylum class order family group species. Ch. 2 – Atoms and Molecules Valence electrons vs. valence Valence electrons are how many electrons are already there in the outer orbital/valence shell. Valence is how many electrons are needed to get to 8. Bonds Covalent – “Share”. o Polar covalent bonds – One element is more electronegative than the other. o Nonpolar covalent bonds – Often symmetric. Ionic – “Take”. Hydrogen – More like magnetic attractions; atoms are not being shared. Covalent > ionic > hydrogen bonds in strength, in general. Isotopes: Atoms with the same number of protons but a different number of neutrons. Q: According to the octet rule, the distribution of electrons in a sulfur atom (atomic #16)’s orbitals is...? - 2, 8, 6 (2 in first level, 8 in second, 6 in last). Q: If the hydroxide concentration of a solution is 10-4, the hydrogen ion concentration is: - 10-10 (Difference between 10-14 and 10-4 = 10-10). Ch. 3 – Water Hydrophilic – Water-loving, dissolves in water, polar. Hydrophobic – Water-hating, doesn’t dissolve in water, nonpolar. Solvent – Dissolves things; often water. Solute – Gets dissolved by solvent; non-water. Q: Does an acid have more or less H+ ions compared to a base? - More. Q: Which portion of pH scale are acids and which are bases? - Below 7 is acidic, above 7 is basic, and exactly 7 is neutral. Q: The cohesiveness of water molecules is due to what type of bond? - Hydrogen bonds. (The properties of water are due to hydrogen bonds) Q: Name some properties of water. - Cohesion, adhesion, surface tension, high specific heat, expands upon freezing, universal solvent. Ch. 4 – Functional Groups, Isomers, and Carbon Isomers: Structural isomers differ in shape (flat vs. branched), geometric isomers differ in arrangement about a double bond, and enantiomers are mirror images of each other. Functional groups: The functional groups are certain molecules attached to organic molecules: hydroxyl – OH carbonyl – CO (alcohols) (ketones, aldehydes) carboxyl – COOH amino – NH2 groups) sulfhydryl – SH phosphate – PO4 methyl – CH3 (acids; “carbonyl” + “hydroxyl” = “carboxyl”) (amines; only one with N; amino acids have amino and carboxyl (thiols; only one with S) (ATP; only one with P) (methylated compounds) Q: What type of bonds does carbon form? - Covalent. Q: Do isomers (geometric isomers, structural isomers, enantiomers) have equal biological activity? - Nooooo~! Ch. 5 – Macromolecules Carbohydrates – Sugars aka polysaccharides. Also, glycogen (how animals store energy), starch (how plants store energy), and cellulose (plant cell walls). Lipids – Fats, phospholipids, and steroids. Nucleic acids – DNA and RNA. Proteins Protein structure (and what bonds hold them together) 1. Primary (the sequence of amino acids) 2. Secondary (pleated sheet or coiled due to hydrogen bonds; causes hair proteins to be either wavy or curly :D) 3. Tertiary (3-D shape due to R groups attracting; bedhead) Most proteins stop at tertiary structure. 4. Quaternary (multiple tertiary structures; polypeptide bonds form a chain; a right mess) Examples of proteins that have quaternary structure: collagen (in the skin) and hemoglobin (in the blood) Denaturation – Proteins become denatured/lose their function due to (1) pH, (2) temperature, (3) a change in salinity, or (4) chemical interference. Yes, several of these are essentially the same thing; no, I don’t know why they’re considered separate categories. Bear with me, here. :D Q: Which macromolecule must have C, H, and O in a 1:2:1 ratio? - Carbohydrates. Ch. 6 – Cellular Organelles Mitochondria – In eukaryotic cells, the mitochondrion produces massive amounts of ATP through cellular respiration, thus its nickname “the powerhouse”. ATP (and the PO4 functional group) – Adenosine triphosphate (ATP) contains a lot of energy in its bonds because the three phosphates (PO4) are negatively charged and desperately want to get away from each other. Hypertonic, hypotonic, isotonic Hypertonic means more solute than solvent/water. Keywords include “swell”, “burst”, and “lyse”. Hypotonic means more solvent/water than solute. Keywords include “shrink” and “cremate”. Isotonic means equal solvent/water and solute. Ch. 7 – Membrane Structure and Function Phospholipid bilayer: The phospholipid bilayer, which contains hydrophilic/polar heads and hydrophobic/nonpolar tails, is the major component of the cell membrane. Membrane transport Passive transport o Diffusion (high to low concentrations/with the concentration gradient) o Facilitated diffusion (diffusion with the help of a protein) o Osmosis (diffusion of water specifically) Active transport o From low to high concentrations/against the concentration gradient. Junctions Tight junctions (don't allow anything through) Anchoring junctions (keep cells attached while they communicate) Gap/communicating junctions (allow the transfer of proteins between cells) Ch. 8 – Metabolism Anabolic – Building up (think anabolic steroids) Catabolic – Breaking down (think glycolysis breaks down glucose) The Laws of Thermodynamics 1. Energy cannot be created nor destroyed, only transferred. 2. Every transfer of energy increases the entropy of the universe. Gibbs free energy – Delta G is negative if energy is given off (spontaneous, exergonic), positive if energy is consumed (nonspontaneous, endergonic). Think of delta G as the amount of energy needed; if it is negative, none is needed. Activation energy (Ea) – The initial amount of energy needed to start a chemical reaction. Enzymes can lower this Ea barrier. Catalyst – Speeds up a reaction without being consumed by the reaction. Active site – Where the substrate is supposed to bind, but can be blocked by a competitive inhibitor. Q: How does a competitive inhibitor work? - By blocking the correct substrate from being able to fully attach to the enzyme/catalyst. Ch. 9 – Cellular Respiration Glycolysis: Lyses glucose; makes two pyruvates per glucose molecule. Pre-citric acid cycle & citric acid cycle: At the end of glycolysis, the pyruvates: If oxygen is present, go into the mitochondria and enter the Krebs/citric acid cycle, which adds electrons onto the electron shuttles (reduces them). The ETC is activated. If oxygen is not present, do not continue into the mitochondria. Cell respiration stops and fermentation begins instead. Electron transport chain: The electron shuttles combined with H+ ions go through the electron transport chain and power chemiosmosis, creating a large amount of ATP. Ch. 10 – Photosynthesis Cellular respiration backward! Plants have the ability of carbon fixation (changing inorganic carbon into organic carbon). Ch. 12 – The Cell Cycle and Mitosis Mitosis happens in the somatic (non-sex) cells. Starts diploid, produces 2 diploid clone cells. [do cell cycle and mitosis on whiteboard] Ch. 13 – Meiosis Meiosis occurs in the sex cells/gametes (eggs and sperm). Starts diploid, produces 4 haploid daughter cells. [do meiosis on whiteboard] Ch. 14 – Mendelian Genetics and Others [do Punnett squares on whiteboard] Epistasis – One gene affects the expression of another gene (black, brown, and yellow labradors; a yellow lab has a second gene that inactivates its coat color gene). Pleiotropy – One gene, multiple phenotypes (e.g. cystic fibrosis). Polygenic inheritance – Multiple genes, one phenotype (e.g. hair color, eye color, skin color). Complete dominance – The default; both AA and Aa would give the dominant phenotype (red x white flower = red heterozygote). Incomplete dominance – The heterozygote Aa gives a halfway in-between phenotype (red x white flower = pink heterozygote). Codominance – The heterozygote gets both phenotypes expressed fully (A blood x B blood = AB blood). Ch. 15 – Sex-Linked Traits [do sex-linked Punnett squares on whiteboard] Ch. 16 – DNA Replication/RNA Synthesis DNA is synthesized during the S stage of the cell cycle. This chapter zooms in on that stage to talk about what actually happens. [do DNA replication on whiteboard] Enzymes used in DNA replication Helicase – Unwinds the DNA. Single-stranded binding proteins – Stabilizes the unwound strands. Topoisomerase – Prevents overwinding and twisting of not-yet-unwound strands. Primase – Creates the primer, which lays down the first few nucleotides. DNA polymerase – Continues laying down nucleotides, also proofreads the nucleotides that have already been added. Ligase – Ties back up the DNA strands and Okazaki fragments when they are done being replicated. Q: Where does DNA replication occur? Wherever the DNA is (nucleus in eukaryotes, cytoplasm in prokaryotes). Ch. 17 – Transcription and Translation [do transcription and translation on whiteboard] The Central Dogma of Biology – DNA transcription RNA translation proteins Ch. 18 – The Regulation of Gene Expression An operon contains the operator (the actual gene switch), promoter, and the genes it controls. Operons can be repressible or inducible: If they are repressible, they are on (you can’t repress something that hasn’t begun!). If they are inducible, they are off (you can’t start something that’s already begun!). Repressors, if active, can turn operons off by binding to their operators and blocking RNA polymerase from touching (and thus translating) the genes. Ch. 22 – Descent with Modification: Darwin and Others Sexual Selection Intersexual (“between different sexes”) = Females prefer certain mates. Intrasexual (“among the same sex”) = e.g. Males compete with one another; one becomes alpha and mates with the female. Sexual dimorphism – The differences between males and females of the same species. 3 Key Points to Natural Selection Individuals do not evolve, populations evolve. Natural selection only works on heritable traits with variation in the population. Evolution is not working towards a specific goal or “perfect” organisms. Homologous structures – Structures that evolved from a common ancestor (e.g. human hands and bat wings). Vestigial structures – Structures that have lost their ancestral functions but are still present (e.g. a whale’s pelvic bone). Adaptation – Traits with useful roles are selected for in natural selection. Jean Baptiste Lamarck – Hypothesized that acquired traits can be inherited (e.g. thought giraffes progressively stretched their necks farther and farther and could pass down these longer necks to their children) Charles Darwin – Wrote On the Origin of Species; sailed to the Galapagos Islands and noticed profound differences in the finches there, specifically their beaks. He proposed these finches all came from a common ancestor but had evolved to eat their own type of food source on the island. Theory of Evolution Change through time. Descent with modification. Genetic changes in population over time. Unifying theory of biology. - Note: A scientific theory is much more heavily evidenced than the connotation of “theory” used in everyday conversation! For example, gravity is also a theory. Q: How does natural selection cause change in a population? - By selective advantage; certain individuals will have more suitable characteristics for their environment and will tend to be able to reproduce more often. Q: What does natural selection act on in the population? - Inherited characteristics that lead to an advantage in the environment. Q: What fields have shown evidence to support natural selection as a mechanism of evolution? - Biology, geology, chemistry, physics. Ch. 23 – The Evolution of Populations Null hypothesis vs alternative hypothesis Null hypothesis: no difference (e.g. “White tigers have the same lifespan as orange tigers”). o “Null” means “zero” in other languages, so “zero difference”. Alternative hypothesis: there is a difference (e.g. “White tigers live shorter than orange tigers”). Limits of natural selection Selection can only act on existing variation in a population. Evolution is limited by historical constraints. Adaptations are usually compromises. Natural selection interacts with chance/random events and the environment. Microevolution Many things can cause change in a population: Mutations – A permanent change in the DNA sequence of a gene (e.g. having blue eyes). Natural Selection – Selective advantage of those individuals better suited for the environment. Genetic Drift – Change in allele frequency due to random sampling. Gene Flow – Moving genes from one population to another. Hardy-Weinberg p + q = 1 (allele frequencies) p2 + 2pq + q2 = 1 (genotype frequencies) p = dominant allele frequency q = recessive allele frequency p2 = homozygous dominant frequency 2pq = heterozygote frequency q2 = homozygous recessive frequency Hardy-Weinberg: 5 Assumptions 1. No natural selection. 2. No mutation. 3. No gene flow. 4. Completely random mating. 5. Large population. - The Hardy-Weinberg principle is a “null hypothesis” to check for evolution; it is almost always violated by real populations. Hardy-Weinberg Problems A population of 100 butterflies has a dominant brown color and a recessive white color. 1. If the frequency of the brown allele is 0.8, what is the frequency of the white allele? p = 0.8 p+q=1 q = 1 – 0.8 = 0.2 2. Calculate the predicted frequencies of the genotypes if population is at HardyWeinberg equilibrium. p= 0.8, q= 0.2; genotype frequency equation= p2 + 2pq + q2 = 1 p2 = (0.8)2 = 0.64 2pq= 2(0.8)(0.2) = 0.32 q2 = (0.2)2 = 0.04 0.64 + 0.32 + 0.04 = 1 3. In the butterfly population, 25% are dominant homozygous, 50% are heterozygous, and 25% are homozygous recessive. Find p and q for this population. Frequency of homozygous dominant = p2 = 0.25, p = √0.25 = 0.5 Frequency of homozygous recessive = q2 = 0.25, q = √0.25 = 0.5 Frequency of heterozygous = 2pq = 0.5 Ch. 24 – The Origin of Species Speciation – The formation of new, distinct species. Allopatric speciation – “Different country”, aka two species developing in separated areas. Sympatric speciation – “Same country”, aka two species developing in the same area. Reproductive barrier – Anything that inhibits reproduction. Pre-zygotic barriers Post-zygotic barriers Macroevolution – Evolution of taxonomic groups over long periods. Q: What are some different types of post-zygotic barriers? - Reduced hybrid viability or fertility, or hybrid breakdown.