bio207 Exam 1

The Big Ideas From Chapter 1: How do we recognize life? Hierarchical structure of life Unity and diversity of life Biology as a scientific discipline Hypothesis v. a theory A. How do we recognize life Water bears 0.1-0.5mm long Lack circulatory and respiratory system Can reduce body water from 85% to 3% for up to 10 years Are they alive at 3% body water? Measure oxygen uptake for aerobic (using oxygen) metabolism (sum of chemical reactions in body, living organisms run chemical reactions in their cells) Measure anaerobic (without oxygen) metabolism Measure cell division Measure waste production Seven Characteristics of Life Cells and organization Energy use and metabolism Response to environmental changes Regulation and homeostasis Growth and development Reproduction Biological evolution (population level) B. Hierarchal Structure of Life Life has levels of organization (Figure 1.6) 1. Atoms2. Molecules3. Cells C. Unity and Diversity of Life Can classify/group organisms by how they differ or by what they have in common (Figure 1.12) For example, look at cell structure differences: Eukaryotes: Complex internal cell structure (Figure 4.5) Prokaryotes: Simple internal cell structure (Figure 4.4a) How are eukaryotes and prokaryotes related? Look at a trait that all groups share Carl Woese: looked for “relatedness” by gene sequencing The idea: more similar gene sequences= the more closely related Woese’s Data: **Look at Chase’s picture Archaeans (prokaryotes) are more closely related to eukaryotes than to bacteria (prokaryotes) Molecular structure is the key to understanding the diversity of life D. Biology as a Scientific Discipline Observe a national phenomenon Form a hypothesis (=a tentative explanation) Test hypothesis using the scientific method Hypothesis v. a Theory Hypothesis must be “testable” Observations/experiments support or do not support (not prove/disprove) the hypothesis If lots of data support a hypothesis, it becomes a theory Often you just manipulate one variable Compare manipulation to control Analyze data for statistically significant differences Test Case: Guarding behavior in social mammals Live in colonies of 3-30 individuals 1 dominant female and 1 dominant male produce most kids 2-15 adults help raise kids Dig below ground for prey Observations: One individual of group does not feed He/she stands upright in an elevated area He/she produces loud sounds when predator is near At the sound, all animals return to the burrows Ideas: The standing individuals are guarding the group or, Guarding benefits the group, but costs the guard because he/she doesn’t eat when guarding produce a hypothesis to test one of these ideas manipulating a variable is optional Finally, complicated behaviors can be affected by a single gene. E.g: A gene, fosB, controls nurturing behavior in mice. Females with mutant fosB don’t clean their pups, nurse them or keep them warm. Chapter 2: The chemical basis of life Atoms Periodic table Elements in biological systems Types of bonds Water pH Why is lie carbon-based? Organisms are a collection of molecules. Molecules are formed of atoms. 0463552—Atomic #- number of protons He—symbol 4.0026—Atomic mass 02—Atomic #- number of protons He—symbol 4.0026—Atomic mass Isotope: atoms of an element with different #’s of neutrons. # protons determines the element. # neutrons determines the isotope. Atomic mass: the average mass of all isotopes in their naturally occurring proportions. Electrons travel in an energy level or “shell”. Electrons in outer shell are valence electrons. # valence electrons determines the atom’s chemical reactivity. Atoms like to fill their outer shell. Atoms that gain or lose electrons form ions. Cations: net + charge (e.g., Na+, fig. 2.12) Anions: net – charge Mole: Avogadro’s Number—measures amounts of atoms in moles 1 mole contains 6.022 X 10^23 atoms The Periodic Table: Columns= elements with similar properties Rows= number shells Organisms are mostly C, H, N, and O Small quantities of some other elements are required for life Molecule: 2 or more atoms bonded together Compound: atom containing 2 or more elements 3 Kinds of Bonds: 4a. Covalent Polar covalent 4b. hydrogen 4c. Ionic 4a. Covalent Bonds: atoms share pairs of electrons Strong bonds 1 pair electrons shared= single covalent bond 2 pairs shared= double covalent bond 3 pairs shared= triple covalent bond Nitrogen N has 5 electrons in outer shell and needs 8 (= octet rule). 2 N atoms share a triple covalent bond strong, hard to break. In covalent (nonpolar) bonds, electrons are shared equally between bonding atoms. In polar covalent bonds, electrons are not shared equally. One atom hogs them. Polar covalent bonds formed by differences in electronegativity (EN) of the bonding atoms. EN= an atom’s ability to attract electrons. Measured in “Pauling units” (no dimensions). Scales from 0.7 to 4.0 General Pattern of how electronegativity increases across the periodic table: 800100145415 Relative EN values: H= 2.1 C= 2.5 N= 3.0 O= 3.5 Difference of EN of the 2 bonding atoms determines bond polarity. If the difference in EN is small (0-0.4), bond is nonpolar covalent. If the difference in EN is intermediate (0.4-2.0), bond is polar covalent. There is a spectrum of bond polarity The difference in EN of oxygen and hydrogen is 1.4; the bonds are polar covalent. O takes on a net – charge; H a net + charge. Water is a dipole. Molecule polarity depends on bond polarity and geometry. Three examples: A. Water B. Carbon dioxide C. Phospholipid A. Water Big difference in EN so bonds are polar. Bond angles concentrate (-) charges on one side so the molecule is polar. B. Carbon Dioxide Difference in EN= 1 so the C O bonds are polar. Molecule is linear so the bonds oppose each other. Molecule is nonpolar. C. Phospholipid Polarity can vary across a big molecule. Amphipathic molecules have polar regions and nonpolar regions. Amphipathic phospholipids spontaneously form bilayers (membranes) in water. 4b. Hydrogen bonds H atom in a polar molecule is attracted to an electronegative atom in another polar molecule. Polar molecules like to interact and form H bonds. Individual H bonds are week. Many H bonds together are strong. 4c. Ionic bonds Form when there is a big difference in EN = 2.0-3.3 Electron is almost completely transferred to the high EN atom. Example: Na+ and Cl- form NaCl through ionic bonds. Water, which has an uneven distribution of charge across the molecule, is a dipole. Water is essential for life. Water molecules are attracted to each other (cohesion) and other types of molecules (adhesion). Water is the primary solvent in organisms. Hydrophilic molecules: contain many polar bonds and “like” to interact with H2O. Hydrophobic molecules: don’t contain many polar bonds – don’t interact with H2O. Water is the primary solvent in living organisms. H2O is thermally stable (= high specific heat). It’s freezing or boiling point changes when a solute is added. Pure water ionizes: H2OH+ + OH- (OH- is a hydroxide ion) pH: the H+ concentration, or [H+] pH= -log10[H+] At pH = 7, [H+] = [OH-] Acids: release H+ into solution Bases: lower H+ concentration in solution Buffers: minimize pH fluctuations in solutions when acids or bases are added. Organisms regulate pH; and vary it even within different cell compartments. Silicon is the 8th most common element in the universe by mass. Common in the earth’s crust. Same valence # as C Silicon life might look like animated crystals. Silicon atoms are: BIG so bond strength is weak. Don’t form double or triple covalent bonds. Forms crystal lattices instead of chains. Si compounds are generally highly-stable and not reactive. Chapter 3: Organic Chemistry Organic molecules contain carbon 4 valence electrons in carbon C-C and C-H bonds: nonpolar C-O and O-H bonds: polar Functional groups: Groups of atoms with special chemical features/functions NH2amino group COOHcarboxyl group Four major types of organic molecules and macromolecules Carbohydrates Lipids Proteins Nucleic Acids 1. Carbohydrates = Cn(H2O)n Simplest sugars: Monosaccharides (MS) Hexose (6C) Glucose (C6H12O6) Pentose (5C) Ribose (C5H10O5) Deoxyribose (C5H10O4) In solution, MS form rings Disaccharides: link 2 MS by dehydration reaction Link many MS = polysaccharide Starch: some branches, energy storage in plants. Glycogen: highly branched, highly soluble, short-term energy storage in animals. Cellulose: unbranched, linear, structural (fiber) in plants. 2. Lipids: made of H and C Nonpolar molecules Insoluble in water Three kinds of lipids: A. Fats: energy storage, structural support. B. Phospholipids: form cell membranes. C. Steroids: e.g., cholesterol and steroid hormones. Fatty Acids: 2 types Saturated: C’s linked by single covalent bonds. Solid at room temperature. Unsaturated: One or more double bonds like C’s. Liquid at room temperature. Phospholipids = glycerol + 2 fatty acids + phosphate group + a charged nitrogen containing molecule Steroids Four interconnected C rings Cholesterol, estrogen, testosterone Triglyceride, phospholipid, steroid, and carbohydratebe able to tell the difference Given their chemistry, why do you think that plants generally store energy as carbohydrates, but animal generally store energy as fat? 3. Proteins Contain C, H, O, N and usually S Proteins consist of 1 or more polypeptides Polypeptides are polymers made of amino acids Be able to recognize the structure of an amino acid NH2=amino group, alpha carbon, side chain underneath the alpha carbon, and a carboxyl group. *Look at picture from Chase In solution at pH ~ 7, the amino group accepts a H+ (base), and the carboxyl group donates a H+ (acid). Side chains are structurally diverse. Peptide bonds link amino acids Peptide bondcovalent, between carboxyl and amino groups Polypeptides are linear chains of amino acids C-terminus=carboxyl group N-terminus=amino group Proteins have levels of structure Primary structure: amino acid sequence (determined by gene sequence) Cow…**get the rest from Chase Secondary structure: repeating folding patterns stabilized by hydrogen bonds Alpha helices (spirals) Beta sheets (pleated) Some regions don’t either – just randomly coil Tertiary structure: Polypeptide folds into a 3-D shape This may be the final level of structure Quaternary structure: 2 or more polypeptides associate; form a functional multimeric protein. 5 factors promote protein folding/stability: (figure 3.18) H bonds Ionic bonds (between oppositely-charged side chains) Hydrophobic effects: nonpolar amino acids fold to center of protein Van der Waals forces: weak attractive force if atoms are an “optimal” distance apart Disulfide bridges (S-S bonds) 4. Nucleic Acids Are polymers of nucleotides Store, express, and transmit genetic information Chapter 11: DNA Structure and Replication DNA structure Experiments identifying DNA DNA replication An “information molecule” must: Contain necessary information Be passed to offspring Be variable, but still accurate DNA has levels of structure (Fig. 11.5) The top of the molecule has 1. nucleotides, then they are covalently bonded to form a 2. strand, two strands are linked together through hydrogen bonds to form a double helix, the 3. double helix is wrapped around proteins, histone proteins, and if you continue compaction you get into a 4. chromosome. DNA + RNA are polymers made from nucleotides. Nucleotide Fig. 11.6, 11.7 They have a phosphate group, 5 carbon sugar, and a nitrogen base: single or double ring of C and N Carbons in sugar labeled “prime” (Fig. 11.7) Two kinds of bases: Single ring bases: pyridines Cytosine Thymine Uracil Double ring bases: purines Guanine Adenine DNA is missing an O at the 2 prime C (Fig. 11.6), RNA has the O at the 2 prime 5 prime carbon covalently bonded to a phosphate group (Fig. 11.7) Be able to tell difference b/w nucleotide and amino acid, glucose and carbohydrate, etc. Be able to recognize this stuff. Phosphate group connects to the 3 prime of the next sugar by a covalent bond between P and O (Fig. 11.8) The backbone (Fig. 11.8) Alternates phosphates and sugars Is the non-variable part of DNA Is (-) charged A strand is linear All the sugars in a strand are oriented in the same direction This strand, top to bottom, is 5 prime to 3 prime The base sequence is the variable part of DNA (stores information, Fig. 11.8) The bases of two DNA strands H bond; base pairing is specific (Fig. 11.10) 2 H bonds for AT; 3 H bonds for GC (Fig. 11.10) AT/GC base pairing keeps width consistent. Two strands of DNA are antiparallel The strands are complementary: one sequence tells you the other DNA forms a right-handed, repeating, helical structure (-) phosphate groups (negatively charged) are on the outside, interacting with water Minor groove Major groove: proteins attach 2. How was DNA identified? 2 Experiments 2A. Frederick Griffith’s 1920’s S. pneumonia. Causes pneumonia Variation in form: Smooth cells: have an external capsule Rough cells: no capsule Inject in mice Live smooth= pneumonia Live rough= no infection Heat-killed smooth= no infection Heat-killed smooth and live rough= pneumonia and live smooth in blood Griffith concluded: Capsule allows infection A substance from heat-killed smooth transformed live rough to live smooth How? unknown 2B. 1952, Hershey and Chase infect E. coli with the T2 virus (=phage). Phage cost is proteins; which contain S but not P. DNA, inside capsid or “head,” contains P but not S. Label phage with radioactive P and S to track proteins and DNA. Expose bacteria to labeled phage long enough for infection Spinseparates phage and E. coli 32P (DNA) stays with E. coli 35S (protein) stays with empty phage Supports the hypothesis: DNA is the information molecule 3. DNA Replication How does DNA replicate? Original strands= parental strands Newly made strands= daughter strands Semi-conservative replication: each new double-helix has one parental and one daughter strand DNA replication starts at sites called “origins.” Bacteria: one, small, circular chromosome (Figure 11.15). Eukaryotes: multiple, large, linear chromosomes; each has multiple origins of replication **Look at Chase’s notes for picture of DNA replication Replication fork: where parental strands separate Replication bubble: the whole opening Bidirectional replication (Figure 11.15): each new strand forms its 5 prime to 3 prime directions. Parental strands separate and serve as templates (Figure 11.14). New nucleotides are added by AT/GC rule (Figure 11.14) Several proteins are involved (Figure 11.16). DNA helicase: hydrolyzes ATP to unwind the double helix and move fork forward. Single-stranded binding proteins keep parental strands separate. DNA topoisomerase: relieves coiling ahead of fork. Cleaves both strands, swivels the ends and rejoins strands. DNA polymerase: elongates existing strands, starting at their 5 prime end. (Figure 11.20) DNA polymerase catalyzes covalent bonds between nucleotides (Figure 11.17). DNA polymerase elongates strands DNA polymerase needs a starting point. DNA primase makes it: a short strand of RNA called a “primer” (Figure 11.20). DNA polymerase continues the strand from the primer (Figure 11.20) So, 2 new DNA strands are made in each direction from each origin: Leading strand: continuous, 5 prime to 3 prime Lagging strand: made in pieces (= Okazaki fragments) DNA primers makes primase DNA polymerase extends strand (removing primers as it goes) DNA ligase bonds fragments. There are many forms of DNA polymerase! E. coli has 5 forms H. sapiens has 12 Some forms mainly replicate DNA Others remove primers and fill in Others proofread and repair DNA But what about the ends of linear chromosomes? DNA polymerase can’t cope at the tip… Eukaryotic chromosomes have repeat sequences at their ends (telomeres) and a 3 prime overhang (Figure 11.22). Telomerase is a reverse transcriptase: it carries a single-strand RNA template to make a complementary single-strand of DNA. A. Now, the lagging strand is longer. B. Then, primase makes primer. C. Then DNA polymerase fills in segment. Telomerase Is active in cells that actively divide: Embryonic cells Immune system cells Germ cells (stem cells) Not active in most somatic cells Cells with short telomerases stop dividing 90% of human cancers are associated with active telomerase Chapter 12: Gene Expression Introduction Molecular definition of a gene Transcription Eukaryotic transcription Translation tRNA and ribosomes Stages of translation Translation in eukaryotes Central dogma: transcription to translation (or DNA to RNA to protein) Transcription: an RNA copy (= transcript) of a gene is produced. This may be the final product of the gene. Translation: information in messenger RNA (= mRNA) is used to make a protein. Transcription and translation both occur in prokaryotes and eukaryotes (Figure 12.3). Prokaryotes (Figure 12.3): Transcription and translation occur in the cytoplasm. Transcription immediately produces unstable mRNA. Eukaryotes (Figure 12.3): Transcription in nucleus. Transcription makes pre-mRNA, requires processing to form mRNA. Translation in cytosol. 2. Molecular definition of a gene: An organized unit of DNA sequences that: Enables a segment of DNA to be transcribed into RNA. Results in the formation of a functional product. Can categorize genes by product. Structural genes: code for polypeptides. Nonstructural genes: code for RNA product (no translation). 2 Major types: 1. Transfer RNA (tRNA) 2. Ribosomal RNA (rRNA) One scenario of a structural gene (Figure 12.4) **Look at Chase’s picture. Regulatory sequence: Proteins bind here to affect transcription rate. Promoter sequence: Proteins bind to being transcription. Terminator sequence: End of transcription. Second scenario of a structural gene: promoter precedes regulatory sequence. 3. Transcription produces and RNA copy in three stages: Initiation Elongation Termination Initiation Requires sigma factor (a protein). Sigma factor binds to RNA polymerase and to DNA promotor region. RNA polymerase separates DNA strands; forms an “open complex” of 10-15 base pairs (Figure 12.5). Elongation (Figure 12.5) Sigma factor is released Template strand used for mRNA synthesis. Opposite strand is the coding strand, because it has the same sequence as the mRNA (except T instead of U). RNA synthesized in its 5 prime to 3 prime direction which is the DNA 3 prime to 5 prime direction. U not T DNA rewinds behind open complex. Termination (Figure 12.5) RNA polymerase and mRNA transcript dissociate at termination sequence. In prokaryotes, Exam 1 Format: 61 Questions total 26 multiple choice (2.5 pts each) 20 true/false (1 pt each) 15 match (A,B,C,D) (1 pt each) The strand of DNA that is the template varies for different genes (Fig. 12.7). What is the direction of transcription for B? (Fig. 12.7) Your right to left DNA double helix contains antiparallel strands. Either strand can be the template strand. RNA polymerase goes in one direction on the top strand; the opposite direction on the bottom strand. Be comfortable with figure 12.7 4. Eukaryotic transcription: same steps, but more proteins. 3 forms of eukaryotic RNA polymerase Two forms transcribe nonstructural genes. One form transcribes mRNA Requires 5 proteins (called transcription factors) to start Eukaryotic transcription produces pre-mRNA that must be processed Pre-mRNA contains exons and introns Exons – “real” coding sequence. Introns – “intervening sequences” which are transcribed but then removed Splicing removes introns and connects exons (Fig. 12.8). Spliceosome: small nuclear RNA and protein complex of several units that splice mRNA exons. Alternative splicing: a single gene can encode 2 or more polypeptides by varying the splicing. Introns are unusual in eukaryotic rRNA and tRNA sequences. If present, rRNA and tRNA self-splice! Remove their own introns Also, A compound (the 5 prime cap) is covalently bound to the 5 prime end (Fig. 12.10). Allows mRNA to exit nucleus and bind to ribosome. 100-200 adenine nucleotides added to the 3 prime tail (Fig. 12.10). Increases mRNA stability and lifespan in cytosol. 5. Translation: mRNA to protein A group of 3 bases= 1 codon Sequence of bases in a codon specifies an amino acid, or start or stop. Each base is part of only 1 codon (the code does not overlap). Prokaryotic translation (Fig. 12.11) 5 prime ribosomal-binding site. Start codon usually AUG, and codes for an amino acid called MET. Typical polypeptide is a 300 amino acids. Start codon defines the reading frame (p. 248). Adding 1 base shifts the reading frame changes the protein product (p. 248) More than one codon specifies the same amino acid (the code is degenerate). 6. tRNA and Ribosomes 2-D structure of tRNA (Fig. 12.14). Be able to recognize this figure! tRNA molecule coding for each amino acid is unique. An enzyme attaches the right amino acid to tRNAforms charged tRNA. Ribosomes (Figure 12.16) Mix of protein and rRNA Composed of large and small subunits Contain sites doe interacting with tRNA 7. Stages of Translation (Figure 12.18 Prokaryotic Translation) Initiation: mRNA, first tRNA and ribosomal subunits assemble Start codon: AUG Elongation: Polypeptide synthesis as the ribosome travels in the 5 prime to 3 prime mRNA direction Termination: Complex disassembles at a stop codon, releasing completed polypeptide. 8. Different Translation Initiation in Eukaryotes: 5 prime cap allows binding to ribosome Start sequence may contain more bases than AUG Chapter 13: Regulating Genes Introduction Bacteria: usually ctrl transcription Ex: negative control of transcription operon Eukaryotes regulate genes at many levels Many eukaryotes chemically inhibit transcription Controlling Translation with Micro-RNA’s 1. Introduction (Figure 13.2) Cells control/regulate/change the timing and the amount of gene expression Housekeeping genes, or constitutive genes, are always expressed Ex: gene that codes for rRNA is a constitute gene Gene expression can be controlled at the level of Transcription Translation Post-translation (e.g. enzyme inhibition) 2. Bacteria usually control transcription rate (Figure 13.4) Transcription factors: Proteins that affect the function of RNA polymerase Not required to directly bind to RNA polymerase They may inhibit translation (decrease rate of transcription) Repressors, negative control They may increase transcription (increase rate of transcription) Activators, positive control They may need small effector molecules Example: Bacterial regulation of tryptophan synthesis (Fig. 3.14). Tryptophan is a precursor molecule to making serotonin, which makes you sleepy. Trp Operon (Figure 13.12) Negative control of trp operon Repressor binding to O inhibits transcription (of top operon) Repressor requires tryptophan to bind to O Tryptophan is the repressor’s small effector molecule Low levels of tryptophan= inactive repressor = transcription of trp operon (Fig 13.12) High levels of tryptophan, tryptophan binds to repressor. Complex then binds to operator. Helps to stop overproduction of tryptophan Trp operon turned off when product not needed Trp operon is repressible, other operons are inducible. 3. Eukaryotes Regulate Gene Expression on Many Levels (Fig 13.4) 4. Transcription Can be Stopped by Methylation Methylation: adding a methyl group Can be used to stop transcription Methylation Patterns: Are common in plants and vertebrate animals Are inherited (plus needed for normal development) in these groups Modulate gene expression without affecting DNA sequence Change over life in response to environment Change products from genome without changing