Final Exam Study Guide
Final Exam Study Guide Bio 107
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This 20 page Study Guide was uploaded by Rachel Johnson on Sunday December 13, 2015. The Study Guide belongs to Bio 107 at Washington State University taught by William Davis in Summer 2015. Since its upload, it has received 383 views. For similar materials see Biology in Biology at Washington State University.
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Date Created: 12/13/15
Final Exam Study Guide Nucleic Acids DNA: deoxyribonucleic acid Structure Nitrogenous bases Pyrimidines: Cytosine and Thymine Purines: Adenine and Guanine Sugar Deoxyribose Phosphate group Right handed double helix Strands run antiparallel RNA: ribonucleic acid Structure Nitrogenous bases Pyrimidines: Cytosine and Uracil Purines: Adenine and Guanine Sugar Ribose Phosphate group Chargaff’s Rules % A = % T/U and % G = % C *phosphate caps the 5’ end and a base is on the 3’ end DNA and Transformation Genes: carry information that encodes the traits observed in an organism Chromosomes: chemical structures that contain genes; the molecules passed from parent to offspring during reproduction Griffith’s Experiment Studied bacterial strains that caused pneumonia S strain: pathogenic and smooth surface R strain: nonpathogenic and rough surface Experiment results S strain- killed mouse R strain- mouse lived Heat-Killed S strain- mouse lived Heat-Killed S strain and Live R strain- killed mouse Conclusion- something in the heat-killed S strain converted the live R strain Avery’s Experiment Goal: discover the transforming substance in bacteria Experiment Treated five batches of heat-killed S strain with one of five different enzymes RNase: RNA DNase: DNA Protease: Proteins Lipase: Lipids Carboase: Carbohydrates Added the treated S to living R Conclusion- DNA = transforming agent Bacteria release DNA when stressed and that DNA can be absorbed by other cells Proteins Synthesis = dehydration reaction between the carboxyl and amino Breakdown = hydrolysis Enzymes: substances (proteins) that accelerate chemical reactions but are not consumed in the reaction itself Functions Enzymes, immune defense, storage, transportation, hormones, receptors, contracting (support) & motor, and structure Monomer = amino acid Structure Amino → acts as base (proton acceptor) Carboxyl →acts as acid (proton donor) H R group → side chain Gives the unique characteristics Nonpolar amino acids Hydrophobic Location: interior of protein, membranes, etc Gly, Ala, Val, Leu, Ile, Met, Phe, Try, and Pro Polar amino acids (uncharged) Hydrophilic Ser, Thr, Cys, Tyr, Asn, and Gln Charged amino acids Hydrophilic Acidic (negatively charged) Asp and Glu Basic (positively charged) Lys, Arg, and His Electrically charged side chains Structure Primary: sequence of amino acids Determines shape and function Secondary: interactions between backbone groups (H bonds) Two types: alpha helix and beta pleated sheet Tertiary: interactions between R groups Found in all proteins Quaternary: interactions between 2+ polypeptides Only found in some proteins Transcription DNA is transcribed into mRNA Codon: three nucleotides that specify one amino acid Redundancy: can be more than one codon per amino acid Start: AUG Stop: UAA, UAG, UGA RNA synthesis by RNA polymerase Leading DNA strand is transcribed Resulting RNA is exact copy of lagging strand only T is switched for U Three stages Initiation: initiation begins at promoter Transcription factors bind to promoter and recruit the RNA polymerase Elongation: RNA polymerase synthesizes in 5’→3’ direction (reads in the 3’→5’ direction) Doesn’t require primer Termination: ends transcription Prokaryotes- involves termination sequences Eukaryotes- associated with RNA processing mRNA Prokaryotes No nucleus so chromosomes and ribosomes are in the cytoplasm Translated into protein as soon as it’s made Eukaryotes Made in the nucleus and is transported to the ribosomes in the cytoplasm Processing pre-mRNA is made during transcription and is modified to mature mRNA before export from the nucleus RNA in eukaryotes Processing 5’ end- capping (addition of a methylated guanine) 3’ end- polyadenylation (addition of a poly(A) tail) Functions: mRNA export, stability, and translation UTR = untranslated region Splicing Removes introns and unites exons Functions Facilitates export of mRNA Allows multiple proteins to be made from one gene Process Branch site in intron = specific RNA sequence Branch site attacks donor site at intron-exon boundary Upstream exon attacks acceptor site on nearest downstream intron Upstream = [←] 5’-; to the left Downstream = -3’ [→]; to the right Regulation Transcription factors General TFs: used for all protein-coding genes Specific TFs: used for a set of protein-coding genes Transcription activation Can occur over long distances (assisted by DNA-bending proteins) Transcription repression Silencers: DNA TF binding sequence Repressors: DNA-binding proteins Works similarly to activation RNA interference RNA inhibits gene expression by typically destroying specific mRNA Translation tRNA Anticodon: base pairs with mRNA codon Amino acid attachment site = 3’ end Charging: amino acid is attached at the opposite end of the tRNA from anticodon Uses anticodon for recognition of specific amino acid Ribosome rRNA plays a catalytic role Ribosomal protein plays a structural role Subunits come in two completely separate parts (large and small) Binding sites = A site, P site, and E site Three stages Initiation Prokaryotes Small subunit binds to Ribosome Binding Site on mRNA Initiator tRNA binds to start codon Large subunit joins small subunit Initiator tRNA is at P site Eukaryotes Only one gene per mRNA Ribosome binds to 5’ end and starts protein synthesis once start codon is reached Elongation Codon recognition tRNA binds to A site Peptide bond formation between new amino acid at A site and polypeptide at P site Transfers polypeptide to A site Translocation tRNA moves from A site to P site Empty tRNA moves to E site and gets released Codons move forward one step Ribosome movement = P site → A site → P site Termination Release factors bind to stop codon in A site Subunits dissociate Mutation Point mutation: change in one base pair Substitution- results in protein the same length Silent- no change Missense- change Nonsense- change to stop codon Insertion and deletion- addition/removal of nucleotides Frameshift- change in number not in a multiple of three Nonframeshift- change in number in a multiple of three Spontaneous changes usually occur during DNA replication Induced changes are due to mutagens (UV light, ionizing radiation, etc) Bacteria Prokaryotes Common cell shapes Spherical (cocci), Rod (bacilli), and Spiral (spiro) Cell walls- protective layer of polysaccharide Features Capsules (halos)- located outside the outer membrane; used for adherence and protection Fimbriae (attachment pili)- long rods extending out from cell; used for attachment and bringing cells together Taxis- directional movement towards an area of advantage Flagella- allows cells to move; push or pull Gram staining Gram positive bacteria- layer of peptidoglycan outside of plasma membrane (2 layers); stains purple Gram negative bacteria- layer of peptidoglycan in between plasma membrane and outer membrane (3 layers); stains pink Contain plasmids (circular and carry small number of genes) Endospores: resistant cells formed around chromosomes in times of stress; protective measure that allows survival for thousands of years) Genetic diversity Rapid division- errors can lead to spontaneous mutations Genetic transfer- exchange portions of genome Conjugation (physical contact) On a plasmid (F+) On a chromosome (Hfr) Transduction (phages) Transformation (absorption of DNA) Antibiotic resistance- R plasmids containing resistance genes Antibiotics work by inhibiting/disrupting cell wall formation and gene expression Becomes an arms race between bacteria and antibiotics Cells Two major techniques for studying cells Cell fractionation- allows the study of individual cell components Involves homogenization and centrifugation Microscopy Resolution: the ability to see something, inversely related to the wavelength of light or electrons used to create the image Light microscopy (LM)- uses photons Electron microscopy (EM)- uses electrons Scanning EM- view cell surface Transmission EM- view cell interior Cell types- eukaryotic and prokaryotic Common features Plasma membrane, cytosol, chromosomes, and many others Differing features Prokaryotes- no membrane bound organelles, DNA in nucleoid region, and possession of cell wall Eukaryotes- membrane bound organelles, DNA in nucleus, and don’t always possess a cell wall Animal- lysosomes, centrosomes, and flagella Plant- chloroplasts, central vacuole, cell wall, and plasmodesmata Organelles- allow cell to compartmentalize and specialize functions Nucleus Houses chromatin, includes nucleoli, and surrounded by nuclear envelope supported by the nuclear lamina Endomembrane system Functions: protein synthesis and transport; lipid metabolism and transport; and detoxification of poisons and drugs Endoplasmic Reticulum (ER) Smooth Functions: lipid synthesis, drug detox, and calcium storage Rough Functions: protein synthesis, folding, and glycosylation; vesicular transport; and some membrane synthesis Golgi Body Two faces- cis (receiving) and trans (shipping to downstream destinations) Functions: protein modification, storage, and sorting and carbohydrate synthesis Lysosome Two major functions: phagocytosis (digesting food) and autophagy (breaking down damaged organelles) Vacuoles- perform a variety of functions in different kinds of cells Food vacuoles- formed by phagocytosis and fusion with lysosomes Contractile vacuole- pumps out excess water Central vacuole- stores organic compounds and water Endosymbiotic theory- mitochondria and chloroplast arose from the engulfment of prokaryotes Mitochondria Double membrane structure Functions: ATP production and programmed cell death Chloroplasts Double membrane structure Key features = thylakoids, granum, and stroma Function: sugar production from CO an2 water using light energy Peroxisomes Single membrane structure Functions: degrade fatty acids, detox harmful compounds, and neutralize oxidative radicals through oxidation Cytoskeleton Functions: provides cell shape and organelle support; facilitates cell motility and vesicular transport Three major types of fibers Microtubules Functions: maintenance of cell shape, cell motility, chromosome movement during cell division, and scaffolding for ER structure Microfilaments Functions: define cell size, maintenance of cell shape, changes in cell shape, muscle contraction, cytoplasmic streaming, cell motility, and cell division Intermediate filaments Functions: maintenance of cell shape, anchorage of nucleus and certain other organelles, and formation of nuclear lamina Membranes Lipids- made of C, H, and O (hydrophobic) Hydrocarbons- made of C and H Serve as energy storage molecules (high energy density) Isomers Structural- differ in covalent arrangement Cis/Trans- differ in spatial arrangement Cis: similar molecules are on the same side of the C backbone Trans: similar molecules are on opposing sides of backbone Fats Functions: storage and structure Synthesized by dehydration reaction between fatty acids and glycerol to form triacylglycerol Three fatty acids linked to glycerol via bond between hydroxyl and carboxyl Saturated fats- saturated with H Features: no double bonds, solid at room temperature, highest energy density possible, and found in animal products Unsaturated fats- unsaturated with H Features: one or more double bonds, liquid at room temperature, and found in plant products Trans fats- made in process of hydrogenation Made by food industry to increase shelf life Less reactive than natural fats Phospholipids- glycerol backbone, two fatty acids, and a phosphate group Hydrophobic tail and hydrophilic head Lipid bilayers Phospholipids line up so tails are on inside and heads are on the outside (forms two layers) Fluid mosaic model- phospholipids can move within membrane Lateral movement: side to side (very frequent) Flip flop: moving from one face of the membrane to the other (about once a month)- flipase aids in movement Factors affecting fluidity Temperature- ↑ temp ↑ fluidity, ↓ temp ↓ fluidity # of unsaturated hydrocarbons- ↑ amount ↑ fluidity, ↓ amount ↓ fluidity Cholesterol- reduces fluidity at moderate temperatures and prevents solidification at low temperatures Membrane permeability Water- polar molecule, high dielectric constants results in solubility Water soluble: polar molecules/ionic molecules; need channels to cross membrane Oil (lipid) soluble: nonpolar molecules; don’t need channels to cross Easily cross membrane- hydrophobic molecules; small, uncharged, and nonpolar molecules Can’t easily cross- hydrophilic molecules; large, charged, and polar molecules Membrane transport Passive transport Diffusion- random movement towards equilibrium; moving from high to low concentrations Facilitated diffusion- requires proteins, but not energy Active transport- solute moves up its gradient; requires proteins and energy Channel proteins- corridor for solutes to pass through Aquaporins: facilitated diffusion of water Ion channels: facilitated diffusion of ions Carrier proteins- revolving door for solutes Glucose transporter: facilitated diffusion of sugar Sodium-potassium pump: active transport Cell Signaling Types of differentiated cells Muscle- used to generate force for movement, pumping fluids, etc Neural- used for communication and signaling Skin- used to separate organism from environment and provide a selective barrier Mesenchymal Stem Cells (MSCs) Precursor cell for many tissues Require extracellular signal to differentiate Stem cells vs differentiated cells Stem cells and differentiated cells- have the same genes and can send/receive signals Stem cells- has potential to become anything (can divide and differentiate) Differentiated cells- can’t divide further and carries out a specific function until apoptosis Cell signaling overview Stage 1: signal receiving (signaling molecule binds to a receptor on the target cell surface) Stage 2: signal transduction (series of chemical changes within the cell) Stage 3: cellular response Signal transduction- often a series of protein chemical transformations Kinase: enzyme that adds a phosphate group to a protein Phosphatase: enzyme that removes a phosphate group from a protein Signal shut down- occurs when response is completed or signal disappears Signal amplification- 10 receptors→100 TK →1001 TK →10000 2F Proteolysis: hydrolysis of peptide chains in a highly controlled manner; promoted by the protein, ubiquitin Proteasome: complex that houses proteolysis Membrane protein recycling- receptor mediated endocytosis Membrane pinches off fatty acids to form a vesicle Vesicle splits in half with ligands in one half and receptor in the other Ligands get broken down and receptors return to cell surface Cell Cycle and Mitosis Centromere: location where the microtubules bind to pull the chromosomes apart Sister chromatids: two copies of the same chromosome Control Checkpoints G 1 cell size, nutrients, growth factors, and DNA damage G 2 cell size and DNA replication M: chromosome attachment to spindle Cyclin proteins- control checkpoint progression Work in conjunction with cyclin-dependent kinase (Cdk) Oncogenes: genes that contribute to cancer when they gain function Tumor suppressor genes: genes that contribute to cancer when they lose function Two major phases Interphase- 3 distinct periods (G1, S, and G2) G 2 chromosomes are duplicated but condensed Mitotic phase- 2 distinct periods (mitosis and cytokinesis) Prophase- DNA condenses, sister chromatids are together, early mitotic spindle forms, and the nucleus is still intact Prometaphase- DNA condenses, nuclear envelope begins deteriorating, and poles form Metaphase- chromatids align at metaphase plate and spindle attaches to each of the chromatids’ kinetochore Anaphase- chromatids are pulled apart Telophase- chromosomes move into each half and cleavage furrow forms Cytokinesis- cell pinches in two DNA Replication Binary fission: replication by division Semiconservative replication: each daughter cell contains one strand from the parent and one newly synthesized strand DNA polymerase: enzyme that catalyzes DNA replication Initiation Occurs at the origin of replication Strands separate at origin, resulting in a replication bubble with two independent replication forks Proteins Helicase: unzips DNA Single strand binding protein: keeps strands separated Topoisomerase: relieves tension ahead of fork Primase: synthesizes a small piece of RNA that’s used to start DNA synthesis Elongation DNA polymerase synthesizes new strands Leading strand synthesis- toward fork; continuous Lagging strand synthesis- away from fork; discontinuous (Okazaki fragments) Termination DNA pol I replaces RNA primers with DNA Ligase seals DNA segments together Error control Exonuclease activity of DNA polymerase (can backtrack to error, remove incorrect bases, and restart synthesis) End of replication problem- DNA polymerase can’t replace 5’ primer with DNA (can lead to gene loss) Preventive measure = telomeres (repetitive sequences added to the end) Added by telomerase Meiosis Haploid cells: contain half the number of chromosomes; sex cells (n) Diploid cells: contain all of the chromosomes; somatic cells (2n) Nonsister chromatids: DNA strands from male and female in a homologous pair Meiosis I- creates two daughter cells with one sister pair in each Meiosis II- creates four daughter cells with one copy of each chromosome Crossing over: nonsister chromatids exchange DNA that codes for the same trait Occurs in prophase I Begins with synapsis, crossing over occurs, and chiasma appears Allele: particular copy/variant of a gene Law of segregation: analysis of two genes on one chromosome Each gamete only carries one allele of each gene Law of independent assortment: analysis of two genes on two chromosomes Alignment and segregation of homologous pairs is random Linkage: a particular combination of alleles that are inherited together due to close positioning on the chromosome Mendelian Genetics Markers: small pieces of genome that have specific properties Blending hypothesis: traits of parents were blended so offspring showed a mix of both P generation (parental): two different purebreds crossed F g1neration (hybrids): “first filial” F g2neration: offspring from crossing F ge1eration “true breeding”: breeding two of the same species that lead to offspring that look the same Dihybrid cross- used to observe two traits Trying to determine if the genes were inherited together Exceptions Incomplete dominance- neither allele is completely dominant Heterozygote has an intermediate phenotype Patterns of allele inheritance Sex-linked: occur on sex chromosomes Autosomal: occurs on any other chromosome Viruses Consist of a RNA/DNA genome and a protein coat Viral capsid- protein shell made of capsomere proteins that protects the genome Viral envelope- membrane containing viral glycoprotein around capsid that is derived from the host cell membrane Aids in recognition and infection of new host cells Host range- specific species and tissues a virus can infect due to cell surface receptors and molecules Range is determined by viral surface proteins and the host surface proteins Reproductive cycles Double stranded DNA viruses Virus enters the host cell and the coat is removed DNA is replicated and capsid proteins are synthesized New viral cells are self-assembled and released No rupture and usually all normal cell functions continue Bacteriophage Lytic cycle Gets rid of host DNA Same process as above only the host cell lyses upon release of new phage Lysogenic cycle Viral DNA is incorporated into the host’s DNA Lies dormant but can become lytic later on Bacteria can try to block infection by cutting phage DNA upon entry using restriction enzymes Metabolism and Enzymes Two types of pathways Catabolic- release energy and matter Anabolic- store energy and matter Energy sources in food = protein, carbohydrates, and fats Energy storage in chemical bonds Based on distance e- in a bond are from the nucleus Further away = increased PE and closer = decreased PE Bond energy increases if e- are well shared (nonpolar bonds) Gibbs Free Energy Related to two states State of product and energy within reactants ΔG = Gp-Gr ΔG = ΔH – T Δ S H = enthalpy, S = entropy, and T = temperature ΔG < 0 → system can do work on the surroundings Spontaneous and runs in one direction Ex: catabolic reactions ΔG > 0 → surroundings must do work on the system for a change to occur Nonspontaneous Ex: anabolic reactions Exergonic reactions Release energy into the surroundings, spontaneous, ΔGr > ΔGp, and keeps going to completion once started Endergonic reactions Absorb energy from surroundings, nonspontaneous, and ΔGr < ΔGp Activation energy: initial energy input needed to start reactions Lowered by enzymes and heat Reaction pathway Active site binds to its substrates, stabilizes transition state and lowers EA, and releases products Change in temperature or pH can denature an enzyme Competitive inhibitors Bind to the active site and compete with the substrates Can be overcome by increasing [substrate] Allosteric inhibitors Bind away from active site but closes it down (lock enzyme in an inactive state) Allosteric activators Bind away from active site but activates it (lock enzyme in an active state) Enzymes usually work in pathways Pathway can be inhibited at any one of the enzymes and intermediates build up from the active enzymes prior to the inhibited one Glycolysis and Oxidative Phosphorylation Redox reactions Reduced = gain e- (oxidizing agent) and oxidized = lose e- (reducing agent) NAD+ = intermediate that moves e- Oxidized form = NAD+ and reduced form = NADH Glycolysis Input: glucose, 2 ATP, 2 NAD+, and 4 ADP Output: 4 ATP, 2 NADH, 2 pyruvate, and 2 H O 2 Regulated by phosphofructokinase Pyruvate oxidation Input: 2 pyruvates 2 CoA, and 2 NAD+ Output: 2 NADH, 2 CO , 2nd 2 Acetyl CoA Citric acid cycle (Kreb cycle) Input: 2 Acetyl CoA, 6 NAD+, 2 FAD, and 2 ADP Output: 6 NADH, 2 FADH , 22ATP, and 4 CO 2 Control of metabolism is dictated by the energy needs of the cell Electron transport chain e- is brought in on NADH or FADH an2 move through four protein complexes e- move downhill in energy Purpose is to release energy in controlled increments Creates a proton gradient that powers ATP synthase when moved across the membrane Photosynthesis Uses energy to form glucose All reactions occur in the chloroplast Light reactions = thylakoid and dark reactions = stroma Light reactions- make NADPH and ATP needed for sugar synthesis as well as O 2rom H O2oxidation Dark reactions (Calvin cycle)- “fix” CO 2nto sugars Phase 1: carbon fixation 3 RuBP (5C) + 3 CO2 → 6 3PG (3C) Phase 2: reduction 6 3PG (3C) + e- → 6 G3P (3C) – 1 G3P (3C) → 5 G3P (3C) Phase 3: regeneration of RuBP 5 G3P (3C) → 3 RuBP (5C) Light creates excited e- in chlorophyll Release energy through heat, fluorescence, or reducing a neighboring molecule Photosynthetic electron transport chain e- flow from water (low energy) to NADP+ (high energy) Photosystem = protein complex that moves e- from low to high energy Photosystem II- creates O 2nd H+ gradient Photosystem I- provide energy to e- for reduction of NADP+ Gradient protons move from stroma to thylakoid
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